Compositions associated with soybean reproductive growth and methods of use

ABSTRACT

Molecular markers associated with soybean reproductive stage, methods of their use, and compositions having one or more marker loci are provided. Methods comprise detecting at least one marker locus, detecting a haplotype, and/or detecting a marker profile. Methods may further comprise crossing a selected soybean plant with a second soybean plant. Isolated polynucleotides, primers, probes, kits, systems, etc., are also provided.

FIELD OF THE INVENTION

This invention relates to compositions associated with reproductivestage in soybean plants and methods of their use.

BACKGROUND

Soybeans (Glycine max L. Merr.) are a major cash crop and investmentcommodity in North America and elsewhere. Soybean is the world's primarysource of seed oil and seed protein. Improving soybean adaptation forvarious growing regions and environmental conditions is crucial formaximizing yields.

There remains a need for means to identify genomic regions associatedwith reproductive stages in soybean plants. The compositions and methodsprovide important tools for use in plant breeding programs to optimizeor maximize the reproductive growth stage, and/or to develop varietiesadapted for various growing regions or environments.

SUMMARY

Molecular markers associated with soybean reproductive stages, methodsof their use, and compositions having one or more marker loci areprovided. Methods comprise detecting at least one marker locus,detecting a haplotype, and/or detecting a marker profile. Methods mayfurther comprise crossing a selected soybean plant with a second soybeanplant. Isolated polynucleotides, primers, probes, kits, systems, etc.,are also provided.

SUMMARY OF SEQUENCES

SEQ ID NOs: 1-512 comprise nucleotide sequences of regions of thesoybean genome, each capable of being used as a probe or primer, eitheralone or in combination, for the detection of a marker locus associatedwith reproductive growth in soybean. In certain examples, Primer1 andPrimer2 are used as allele specific primers and Probe1 and Probe2 areused as allele probes. The SEQ ID NOs provided in the “Region” column ofthe table below are each a genomic DNA region encompassing therespective marker locus. In some examples, the primers and/or probesdetect the polymorphism on based on a polynucleotide complementary tothe genomic region provided here. It is to be understood that thesequences provided are sufficient for one of skill in the art to detecta locus associated with reproductive growth in soybean regardless of theorientation (forward, or reverse) of the strand used for detection.

Primer1 Primer2 Probe1 Probe2 Region SEQ ID SEQ ID SEQ ID SEQ ID SEQ IDLocus NO: NO: NO: NO: NO: S01435-1 1 2 3 4 5 S01239-1 6 7 8 9 10S00780-1 11 12 13 14 15 S06925-1 16 17 18 19 20 S09951-1 21 22 23 24 25S00170-1 26 27 28 29 30 S04059-1 31 32 33 34 35 S07851-1 36 37 38 39 40S11659-1 41 42 43 44 45 S04279-1 46 47 48 49 50 S02211-1 51 52 53 54 55S08942-1 56 57 58 59 60 S05742-1 61 62 63 64 65 S09155-1 66 67 68 69 70S02037-1 71 72 73 74 75 S13136-1 76 77 78 79 80 S17291-001 — 81 82 83 84S13139-1 85 86 87 88 89 S17292-001 — 90 91 92 93 S13146-1 94 95 96 97 98S17293-001 — 99 100 101 102 S17294-001 — 103 104 105 106 S17581-001 107108 109 110 111 S17691-001 112 113 114 — 115 S17701-001 116 117 118 119120 S03703-1 121 122 123 124 125 S17297-001 — 126 127 128 129 S17298-001— 130 131 132 133 S17299-001 — 134 135 136 137 S17300-001 — 138 139 140141 S17301-001 — 142 143 144 145 S17306-001 — 146 147 148 149 S17310-001— 150 151 152 153 S17311-001 — 154 155 156 157 S17312-001 — 158 159 160161 S17313-001 — 162 163 164 165 S17316-001 — 166 167 168 169 S17317-001— 170 171 172 173 S17318-001 — 174 175 176 177 S17322-001 — 178 179 180181 S17326-001 — 182 183 184 185 S17327-001 — 186 187 188 189 S17328-001— 190 191 192 193 S17329-001 — 194 195 196 197 S10746-1 198 199 200 201202 S17331-001 — 203 204 205 206 S17332-001 — 207 208 209 210 S17337-001— 211 212 213 214 S13093-1 215 216 217 218 219 S12211-1 220 221 222 223224 S04555-1 225 226 227 228 229 S08519-1 230 231 232 233 234 S12876-1235 236 237 238 239 S05937-1 240 241 242 243 244 S08575-1 245 246 247248 249 S08669-1 250 251 252 253 254 S11212-1 255 256 257 258 259S00543-1 260 261 262 263 264 S01452-1 265 266 267 268 269 S11993-1 270271 272 273 274 S13446-1 275 276 277 278 279 S00252-1 280 281 282 283284 S04060-1 285 286 287 288 289 S02664-1 290 291 292 293 294 S00281-1295 296 297 298 299 S01109-1 300 301 302 303 304 S13844-1 305 306 307308 309 S05058-1 310 311 312 313 314 S04660-1 315 316 317 318 319S09955-1 320 321 322 323 324 S08034-1 325 326 327 328 329 S10293-1 330331 332 333 334 S03813-1 335 336 337 338 339 S02042-1 340 341 342 343344 S16601-001 345 346 347 348 349 S01481-1 350 351 352 353 354 S11309-1355 356 357 358 359 S11320-1 360 361 362 363 364 S04040-1 365 366 367368 369 S00863-1 370 371 372 373 374 S17151-001 — 375 376 377 378S17153-001 — 379 380 381 382 S17154-001 — 383 384 385 386 S17156-001 —387 388 389 390 S17159-001 — 391 392 393 394 S08590-1 395 396 397 398399 S17242-001 — 400 401 402 403 S17166-001 404 405 406 407 408S17167-001 409 410 411 412 413 S08539-1 414 415 416 417 418 S17178-001 —419 420 421 422 S17179-001 — 423 424 425 426 S17180-001 — 427 428 429430 S17181-001 — 431 432 433 434 S17182-001 — 435 436 437 438 S17183-001— 439 440 441 442 S02780-1 443 444 445 446 447 S12107-1 448 449 450 451452 S03624-1 453 454 455 456 457 S01953-1 458 459 460 461 462 S00111-1463 464 465 466 467 S04180-1 468 469 470 471 472 S01008-1 473 474 475476 477 S12862-1 478 479 480 481 482 S12867-1 483 484 485 486 487S04966-1 488 489 490 491 492 S10631-1 493 494 495 496 497 S01574-1 498499 500 501 502 S16594-001 503 504 505 506 507 S02777-1 508 509 510 511512

DETAILED DESCRIPTION

The timing of soybean flowering and maturity are important agronomicaltraits that are associated with yield. These traits are largely affectedby the genetic response to environmental signals such as day-length andtemperature. Through selective breeding for flowering and maturityphenotypes, soybean varieties have been developed that are ideallysuited for maximizing yield within a particular environment. Fieldtesting for reproductive characteristics is laborious and challenging,and it cannot be accomplished until late in the plant life cycle. Havingmarkers that can be used to select for reproductive growth expedite theintrogression of desired alleles into elite cultivars.

Multiple genetic loci have been identified as containing genes thatcontrol the reproductive growth period of soybean. Relative maturity(RM) in soybean plays a significant role in determining final seedyield, and it is common for seed yield and the length of reproductivegrowth to have a positive correlation. Extending the reproductive periodthrough manipulation of these loci is important for maximizing yieldpotential. However, it is important to evaluate soybean varieties in thecorrect environments. Utilizing markers associated with soybeanreproductive growth that distinguish between early and late alleles,such as early and late alleles for initiation of flowering, provides theability to segregate soybean populations into the correct testingenvironment, without having to conduct a preliminary progeny test on theline to identify an appropriate environment. It is also desirable toincrease genetic diversity by crossing soybeans line with disparatereproductive habits, such as late flowering by early flowering crosses.This process has been utilized with limited success in the past due tothe low frequency of desirable segregates that have a specificreproductive periods for the target area of adaptation environment. Byutilizing molecular markers associated with reproductive growth, abreeder can identify plants in early generations which likely will havereproductive characteristics for the target environment, rather thanhaving to phenotype and select a preferred reproductive growth phenotypein a previous growing season, therefore saving time and other resources.For example, a parent with relative maturity (RM) of 3.1 crossed with asecond parent with RM 1.7 will produce progeny with an expected RM rangefrom about 1.5 to about 3.5. If the breeder is only interested intesting the lines from this population that are <2.0 RM, the breederwould have to grow out a large number of progeny and select only thosethat mature as <2.0 RM. But, using molecular markers associated withreproductive growth, single plants can be selected having a <2.0 RM byselecting preferred locus, allele, haplotype, and/or marker profile. Itis also desirable to increase the amount of time a soybean plant is inthe reproductive growth stage. For example, one could select for anearlier flowering date without affecting the pod maturity.

Nucleotide polymorphisms, including SNPs as well as insertions/deletions(INDELs) have been identified that are closely linked to and in linkagedisequilibrium (LD) with the reproductive growth loci in soybean. Thesepolymorphisms allow for marker-assisted selection (MAS) of these loci,expediting the creation and precise selection soybean plants with adesired reproductive growth phenotype. This will allow for moreprecision in developing varieties tailored to a particular environment.

At least eight loci affecting flowering and maturity, known as E genes(E1-E8), have been identified (see, e.g., Cober et al. (1996) Crop Sci36:601-605; Cober et al. (1996) Crop Sci 36:606-610; Asumadu et al.(1998) Ann Bot 82:773-778; Cober et al. (2001) Crop Sci 41:721-727; Abeet al. (2003) Crop Sci 43:1300-1304; Tasma & Shoemaker (2003) Crop Sci41:319-328; Cober & Voldeng (2001) Crop Sci 41:698-701; Cober & Voldeng(2001) Crop Sci 41:1823-1926; and, Cober et al. (2010) Crop Sci50:524-527). The E1, E2, and E3 loci have been recently cloned and foundto encode a nuclear localized E1 protein (Xia et al. (2012) Proc NatlAcad Sci USA doi/10.1073/pnas.1117982109 E2155-E2164), a GIGANTEAhomolog (Watanabe et al. (2011) Genetics 188:395-407), and a phytochromeA homolog respectively (Watanabe et al. (2009) Genetics 182:1251-1262).Recessive loss-of-function mutant alleles at these three loci canindependently condition earlier flowering phenotypes.

A method for identifying a soybean plant or germplasm having a traitlocus associated with reproductive growth, the method comprisingdetecting at least one allele of one or more marker loci associated withreproductive growth in soybean is provided. In some examples, a traitlocus associated with reproductive growth is a locus associated withreproductive development, time to initiation of flowering (R1), timefrom planting to initiation of flowering (R1), time from emergence (VE)to initiation of flowering (R1), early flowering, length of reproductivegrowth, time from initiation of flowering (R1) to pod fill, length offlowering, time from initiation of flowering (R1) to beginning maturity(R7), time to full bloom (R2), time from first trifoliate (V1) topre-flowering (V6), and the like.

In some examples, the method involves detecting at least one markerlocus associated with reproductive growth in soybean. In some examplesthe method comprises detecting at least one polymorphism within 30 cM ofa marker locus on LG A1 (ch 5), LG A2 (ch 8), LG B1 (ch 11), LG B2 (ch14), LG C1 (ch 4), LG C2 (ch 6), LG D1a (ch 1), LG D1b (ch 2), LG D2 (ch17), LG E (ch 15), LG F (ch 13), LG G (ch 18), LGH (ch 12) LG I (ch 20),LG J (ch 16), LGL (ch 19), LGM (ch 7), LGN (ch 3), and/or LG O (ch 10),or any combination thereof. In some examples the method comprisesdetecting at least one polymorphism within about 0-25 cM, 0-20 cM, 0-15cM, 0-10 cM, 0-5 cM, or about 0-2.5 cM on LG A1 (ch 5), LG A2 (ch 8), LGB1 (ch 11), LG B2 (ch 14), LG C1 (ch 4), LG C2 (ch 6), LG D1a (ch 1), LGD1b (ch 2), LG D2 (ch 17), LG E (ch 15), LG F (ch 13), LG G (ch 18), LGH (ch 12) LG I (ch 20), LG J (ch 16), LG L (ch 19), LG M (ch 7), LG N(ch 3), and/or LG O (ch 10), or any combination thereof.

In some examples the method comprises detecting at least onepolymorphism within about 0-50 kb, 0-100 kb, 0-200 kb, 0-500 kb, 0-750kb, or about 0-1000 kb on LG A1 (ch 5), LG A2 (ch 8), LG B1 (ch 11), LGB2 (ch 14), LG C1 (ch 4), LG C2 (ch 6), LG D1a (ch 1), LG D1b (ch 2), LGD2 (ch 17), LGE (ch 15), LG F (ch 13), LG G (ch 18), LGH (12), LG I (ch20), LG J (ch 16), LGL (ch 19), LGM (ch 7), LG N (ch 3), and/or LG O (ch10), or any combination thereof.

In some examples the method comprises detecting at least onepolymorphism linked to a marker locus selected from the group consistingof S01435-1 on LG A1 (ch 5), S01239-1 and/or S00780-1 on LG A2 (ch 8),S06925-1, S09951-1, and/or S00170-1 on LG B1 (ch 11), S04059-1 and/orS07851-1 on LG B2 (ch 14), S11659-1, S04279-1, S02211-1, and/or S08942-1on LG C1 (ch 4), S05742-1, S09155-1, S02037-1, S13136-1, S17291-001,S13139-1, S17292-001, S13146-1, S17293-001, S17294-001, S17581-001,S17691-001, S17701-001, S03703-1, S17297-001, S17298-001, S17299-001,S17300-001, S17306-001, S17310-001, S17311-001, S17312-001, S17312-001,S17316-001, S17317-001, S17318-001, S17322-001, S17326-001, S17327-001,S17328-001, S17329-001, S10746-1, S17331-001, S17332-001, S17337-001,S13093-1, S12211-1, S04555-1, and/or S17301-001 on LG C2 (ch 6),S08519-1 on LG D1a (ch 1), S12876-1, S05937-1, S08575-1, S08669-1,S11212-1, and/or S00543-1 on LG D1b (ch 2), S01452-1 and/or S11993-1 onLG D2 (ch 17), S13446-1 on LG E (ch 15), S00252-1, S04060-1, S02664-1,and/or S00281-1 on LG F (ch 13), S01109-1, S13844-1, S05058-1 and/orS04660-1 on LG G (ch 18), S09955-1 on LGH (ch 12), S08034-1 and/orS10293-1 on LG I (ch 20), S03813-1 and/or S02042-1 on LG J (ch 16),S16601-001, S01481-1, S11309-1, S11320-1 and/or S04040-1 on LGL (ch 19),S00863-1, S17151-001, S17153-001, S17154-001, S17156-001, S17159-001,S08590-1, S17242-001, S17166-001, S17167-001, S08539-1, S17178-001,S17179-001, S17180-001, S17181-001, S17182-001, S17183-001, S02780-1,S12107-1, S03624-1, S01953-1, S00111-1, S04180-1, and/or S01008-1 on LGM(ch 7), S12861-1, S04966-1, and/or S12867-1 on LGN (ch 3), and S10631-1,S01574-1, S16594-001, and/or S02777-1 on LG O (ch 10), or anycombination thereof.

In some examples the method comprises detecting at least onepolymorphism within about 0-25 cM, 0-20 cM, 0-15 cM, 0-10 cM, 0-5 cM, orabout 0-2.5 cM of a marker locus selected from the group consisting ofS01435-1 on LG A1 (ch 5), S01239-1 and/or S00780-1 on LG A2 (ch 8),S06925-1, S09951-1, and/or S00170-1 on LG B1 (ch 11), S04059-1 and/orS07851-1 on LG B2 (ch 14), S11659-1, S04279-1, S02211-1, and/or S08942-1on LG C1 (ch 4), S05742-1, S09155-1, S02037-1, S13136-1, S17291-001,S13139-1, S17292-001, S13146-1, S17293-001, S17294-001, S17581-001,S17691-001, S17701-001, S03703-1, S17297-001, S17298-001, S17299-001,S17300-001, S17306-001, S17310-001, S17311-001, S17312-001, S17312-001,S17316-001, S17317-001, S17318-001, S17322-001, S17326-001, S17327-001,S17328-001, S17329-001, S10746-1, S17331-001, S17332-001, S17337-001,S13093-1, S12211-1, S04555-1, and/or S17301-001 on LG C2 (ch 6),S08519-1 on LG D1a (ch 1), S12876-1, S05937-1, S08575-1, S08669-1,S11212-1, and/or S00543-1 on LG D1b (ch 2), S01452-1 and/or S11993-1 onLG D2 (ch 17), S13446-1 on LGE (ch 15), S00252-1, S04060-1, S02664-1,and/or S00281-1 on LG F (ch 13), S01109-1, S13844-1, S05058-1 and/orS04660-1 on LG G (ch 18), S09955-1 on LGH (ch 12), S08034-1 and/orS10293-1 on LG I (ch 20), S03813-1 and/or S02042-1 on LG J (ch 16),S16601-001, S01481-1, S11309-1, S11320-1, and/or S04040-1 on LGL (ch19), S00863-1, S17151-001, S17153-001, S17154-001, S17156-001,S17159-001, S08590-1, S17242-001, S17166-001, S17167-001, S08539-1,S17178-001, S17179-001, S17180-001, S17181-001, S17182-001, S17183-001,S02780-1, S12107-1, S03624-1, S01953-1, S00111-1, S04180-1, and/orS01008-1 on LGM (ch 7), S12861-1, S04966-1, and/or S12867-1 on LGN (ch3), and S10631-1, S01574-1, S16594-001, and/or S02777-1 on LG O (ch 10),or any combination thereof.

In some examples the method comprises detecting at least onepolymorphism within about 0-50 kb, 0-100 kb, 0-200 kb, 0-500 kb, 0-750kb, or about 0-1000 kb of a marker locus selected from the groupconsisting of S01435-1 on LG A1 (ch 5), S01239-1 and/or S00780-1 on LGA2 (ch 8), S06925-1, S09951-1, and/or S00170-1 on LG B1 (ch 11),S04059-1 and/or S07851-1 on LG B2 (ch 14), S11659-1, S04279-1, S02211-1,and/or S08942-1 on LG C1 (ch 4), S05742-1, S09155-1, S02037-1, S13136-1,S17291-001, S13139-1, S17292-001, S13146-1, S17293-001, S17294-001,S17581-001, S17691-001, S17701-001, S03703-1, S17297-001, S17298-001,S17299-001, S17300-001, S17306-001, S17310-001, S17311-001, S17312-001,S17312-001, S17316-001, S17317-001, S17318-001, S17322-001, S17326-001,S17327-001, S17328-001, S17329-001, S10746-1, S17331-001, S17332-001,S17337-001, S13093-1, S12211-1, S04555-1, and/or S17301-001 on LG C2 (ch6), S08519-1 on LG D1a (ch 1), S12876-1, S05937-1, S08575-1, S08669-1,S11212-1, and/or S00543-1 on LG D1b (ch 2), S01452-1 and/or S11993-1 onLG D2 (ch 17), S13446-1 on LGE (ch 15), S00252-1, S04060-1, S02664-1,and/or S00281-1 on LG F (ch 13), S01109-1, S13844-1, S05058-1 and/orS04660-1 on LG G (ch 18), S09955-1 on LGH (ch 12), S08034-1 and/orS10293-1 on LG I (ch 20), S03813-1 and/or S02042-1 on LG J (ch 16),S16601-001, S01481-1, S11309-1, S11320-1, and/or S04040-1 on LGL (ch19), S00863-1, S17151-001, S17153-001, S17154-001, S17156-001,S17159-001, S08590-1, S17242-001, S17166-001, S17167-001, S08539-1,S17178-001, S17179-001, S17180-001, S17181-001, S17182-001, S17183-001,S02780-1, S12107-1, S03624-1, S01953-1, S00111-1, S04180-1, and/orS01008-1 on LGM (ch 7), S12861-1, S04966-1, and/or S12867-1 on LGN (ch3), and S10631-1, S01574-1, S16594-001, and/or S02777-1 on LG O (ch 10),or any combination thereof.

In some examples the method comprises detecting at least onepolymorphism closely linked to a marker locus selected from the groupconsisting of S01435-1 on LG A1 (ch 5), S01239-1 and/or S00780-1 on LGA2 (ch 8), S06925-1, S09951-1, and/or S00170-1 on LG B1 (ch 11),S04059-1 and/or S07851-1 on LG B2 (ch 14), S11659-1, S04279-1, S02211-1,and/or S08942-1 on LG C1 (ch 4), S05742-1, S09155-1, S02037-1, S13136-1,S17291-001, S13139-1, S17292-001, S13146-1, S17293-001, S17294-001,S17581-001, S17691-001, S17701-001, S03703-1, S17297-001, S17298-001,S17299-001, S17300-001, S17306-001, S17310-001, S17311-001, S17312-001,S17312-001, S17316-001, S17317-001, S17318-001, S17322-001, S17326-001,S17327-001, S17328-001, S17329-001, S10746-1, S17331-001, S17332-001,S17337-001, S13093-1, S12211-1, S04555-1, and/or S17301-001 on LG C2 (ch6), S08519-1 on LG D1a (ch 1), S12876-1, S05937-1, S08575-1, S08669-1,S11212-1, and/or S00543-1 on LG D1b (ch 2), S01452-1 and/or S11993-1 onLG D2 (ch 17), S13446-1 on LGE (ch 15), S00252-1, S04060-1, S02664-1,and/or S00281-1 on LGF (ch 13), S01109-1, S13844-1, S05058-1 and/orS04660-1 on LG G (ch 18), S09955-1 on LGH (ch 12), S08034-1 and/orS10293-1 on LG I (ch 20), S03813-1 and/or S02042-1 on LG J (ch 16),S16601-001, S01481-1, S11309-1, S11320-1, and/or S04040-1 on LGL (ch19), S00863-1, S17151-001, S17153-001, S17154-001, S17156-001,S17159-001, S08590-1, S17242-001, S17166-001, S17167-001, S08539-1,S17178-001, S17179-001, S17180-001, S17181-001, S17182-001, S17183-001,S02780-1, S12107-1, S03624-1, S01953-1, S00111-1, S04180-1, and/orS01008-1 on LGM (ch 7), S12861-1, S04966-1, and/or S12867-1 on LGN (ch3), and S10631-1, S01574-1, S16594-001, and/or S02777-1 on LG O (ch 10),or any combination thereof.

In some examples the method comprises detecting at least onepolymorphism in a marker locus selected from the group consisting ofS01435-1 on LG A1 (ch 5), S01239-1 and/or S00780-1 on LG A2 (ch 8),S06925-1, S09951-1, and/or S00170-1 on LG B1 (ch 11), S04059-1 and/orS07851-1 on LG B2 (ch 14), S11659-1, S04279-1, S02211-1, and/or S08942-1on LG Cl (ch 4), S05742-1, S09155-1, S02037-1, S13136-1, S17291-001,S13139-1, S17292-001, S13146-1, S17293-001, S17294-001, S17581-001,S17691-001, S17701-001, S03703-1, S17297-001, S17298-001, S17299-001,S17300-001, S17306-001, S17310-001, S17311-001, S17312-001, S17312-001,S17316-001, S17317-001, S17318-001, S17322-001, S17326-001, S17327-001,S17328-001, S17329-001, S10746-1, S17331-001, S17332-001, S17337-001,S13093-1, S12211-1, S04555-1, and/or S17301-001 on LG C2 (ch 6),S08519-1 on LG D1a (ch 1), S12876-1, S05937-1, S08575-1, S08669-1,S11212-1, and/or S00543-1 on LG D1b (ch 2), S01452-1 and/or S11993-1 onLG D2 (ch 17), S13446-1 on LGE (ch 15), S00252-1, S04060-1, S02664-1,and/or S00281-1 on LG F (ch 13), S01109-1, S13844-1, S05058-1 and/orS04660-1 on LG G (ch 18), S09955-1 on LGH (ch 12), S08034-1 and/orS10293-1 on LG I (ch 20), S03813-1 and/or S02042-1 on LGJ (ch 16),S16601-001, S01481-1, S11309-1, S11320-1, and/or S04040-1 on LGL (ch19), S00863-1, S17151-001, S17153-001, S17154-001, S17156-001,S17159-001, S08590-1, S17242-001, S17166-001, S17167-001, S08539-1,S17178-001, S17179-001, S17180-001, S17181-001, S17182-001, S17183-001,S02780-1, S12107-1, S03624-1, S01953-1, S00111-1, S04180-1, and/orS01008-1 on LGM (ch 7), S12861-1, S04966-1, and/or S12867-1 on LGN (ch3), and S10631-1, S01574-1, S16594-001, and/or S02777-1 on LG O (ch 10),or any combination thereof.

In some examples, the method comprises detecting a polymorphism using atleast one marker selected from the group consisting of a marker selectedfrom the group consisting of S01435-1-001 on LG A1 (ch 5), S01239-1-Aand/or S00780-1-A on LG A2 (ch 8), S06925-1-Q1, S09951-1-Q1, and/orS00170-1-A on LG B1 (ch 11), S04059-1-A and/or S07851-1-Q1 on LG B2 (ch14), S11659-1-Q1, S04279-1-A, S02211-1-A, and/or S08942-1-Q1 on LG C1(ch 4), S05742-1-Q1, S09155-1-Q1, S02037-1-A, S13136-1-Q1,S17291-001-K001, S13139-1-Q1, S17292-001-K001, S13146-1-Q1,S17293-001-K001, S17294-001-K001, S17581-001-Q008, S17691-001-Q001,S17701-001-Q001, S03703-1-Q1, S17297-001-K001, S17298-001-K001,S17299-001-K001, S17300-001-K001, S17306-001-K001, S17310-001-K001,S17311-001-K001, S17312-001-K001, S17312-001-K001, S17316-001-K001,S17317-001-K001, S17318-001-K001, S17322-001-K001, S17326-001-K001,S17327-001-K001, S17328-001-K001, S17329-001-K001, S10746-1-Q1,S17331-001-K001, S17332-001-K001, S17337-001-K001, S13093-1-Q1,S12211-1-Q1, S04555-1-Q1, and/or S17301-001-K001 on LG C2 (ch 6),S08519-1-Q1 on LG D1a (ch 1), S12876-1-Q1, S05937-1-Q1, S08575-1-Q1,S08669-1-Q1, S11212-1-Q1, and/or S00543-1-A on LG D1b (ch 2), S01452-1-Aand/or S11993-1-Q2 on LG D2 (ch 17), S13446-1-Q1 on LGE (ch 15),S00252-1-A, S04060-1-A, S02664-1-A, and/or S00281-1-A on LGF (ch 13),S01109-1-Q002, S13844-1-Q1, S05058-1-Q1 and/or S04660-1-A on LG G (ch18), S09955-1-Q1 on LGH (ch 12), S08034-1-Q1 and/or S10293-1-Q1 on LG I(ch 20), S03813-1-A and/or S02042-1-A on LG J (ch 16), S16601-001-Q001,S01481-1-A, S11309-1-Q1, S11320-1-Q1, and/or S04040-1-A on LGL (ch 19),S00863-1-A, S17151-001-K001, S17153-001-K001, S17154-001-K001,S17156-001-K001, S17159-001-K001, S08590-1-Q1, S17242-001-K001,S17166-001-Q006, S17167-001-Q007, S08539-1-Q1, S17178-001-K001,S17179-001-K001, S17180-001-K001, S17181-001-K001, S17182-001-K001,S17183-001-K001, S02780-1-Q1, S12107-1-Q1, S03624-1-Q001, S01953-1-A,S00111-1-A, S04180-1-A, and/or S01008-1-B on LGM (ch 7), S12861-1-Q1,S04966-1-Q1, and/or S12867-1-Q002 on LGN (ch 3), and S10631-1-Q1,S01574-1-A, S16594-001-Q10, and/or S02777-1-A on LG O (ch 10), or anycombination thereof.

In other examples, the method involves detecting a haplotype comprisingtwo or more marker loci, for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,30, or 31 marker loci, or more. In certain examples, the haplotypecomprises two or more markers selected from the group consisting ofS01435-1-001 on LG A1 (ch 5), S01239-1-A and/or S00780-1-A on LG A2 (ch8), S06925-1-Q1, S09951-1-Q1, and/or S00170-1-A on LG B1 (ch 11),S04059-1-A and/or S07851-1-Q1 on LG B2 (ch 14), S11659-1-Q1, S04279-1-A,S02211-1-A, and/or S08942-1-Q1 on LG C1 (ch 4), S05742-1-Q1,S09155-1-Q1, S02037-1-A, S13136-1-Q1, S17291-001-K001, S13139-1-Q1,S17292-001-K001, S13146-1-Q1, S17293-001-K001, S17294-001-K001,S17581-001-Q008, S17691-001-Q001, S17701-001-Q001, S03703-1-Q1,S17297-001-K001, S17298-001-K001, S17299-001-K001, S17300-001-K001,S17306-001-K001, S17310-001-K001, S17311-001-K001, S17312-001-K001,S17312-001-K001, S17316-001-K001, S17317-001-K001, S17318-001-K001,S17322-001-K001, S17326-001-K001, S17327-001-K001, S17328-001-K001,S17329-001-K001, S10746-1-Q1, S17331-001-K001, S17332-001-K001,S17337-001-K001, S13093-1-Q1, S12211-1-Q1, S04555-1-Q1, and/orS17301-001-K001 on LG C2 (ch 6), S08519-1-Q1 on LG D1a (ch 1),S12876-1-Q1, S05937-1-Q1, S08575-1-Q1, S08669-1-Q1, S11212-1-Q1, and/orS00543-1-A on LG D1b (ch 2), S01452-1-A and/or S11993-1-Q2 on LG D2 (ch17), S13446-1-Q1 on LGE (ch 15), S00252-1-A, S04060-1-A, S02664-1-A,and/or S00281-1-A on LGF (ch 13), S01109-1-Q002, S13844-1-Q1,S05058-1-Q1 and/or S04660-1-A on LG G (ch 18), S09955-1-Q1 on LGH (ch12), S08034-1-Q1 and/or S10293-1-Q1 on LG I (ch 20), S03813-1-A and/orS02042-1-A on LG J (ch 16), S16601-001-Q001, S01481-1-A, S11309-1-Q1,S11320-1-Q1, and/or S04040-1-A on LGL (ch 19), S00863-1-A,S17151-001-K001, S17153-001-K001, S17154-001-K001, S17156-001-K001,S17159-001-K001, S08590-1-Q1, S17242-001-K001, S17166-001-Q006,S17167-001-Q007, S08539-1-Q1, S17178-001-K001, S17179-001-K001,S17180-001-K001, S17181-001-K001, S17182-001-K001, S17183-001-K001,S02780-1-Q1, S12107-1-Q1, S03624-1-Q001, S01953-1-A, S00111-1-A,S04180-1-A, and/or S01008-1-B on LG M (ch 7), S12861-1-Q1, S04966-1-Q1,and/or S12867-1-Q002 on LGN (ch 3), and S10631-1-Q1, S01574-1-A,S16594-001-Q10, and/or S02777-1-A on LG O (ch 10), or any combinationthereof. In further examples, the haplotype comprises markers from theset of markers described in Tables 26-46.

In other examples, the method involves detecting a marker profilecomprising two or more marker loci, for example, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, or 31 marker loci, or more. In some examples the method usesmarker assisted selection to stack two or more loci in a soybean plant,cell, seed, or germplasm. In some examples the method uses a markerprofile to produce a soybean plant, cell, seed, or germplasm having adesired predicted flowering time. In some examples the desired predictedflowering time, is a desired flowering time for a specific adaptedgrowing zones or area of adaptability, including but not limited to daylength, latitude, environmental class, management zone, maturity groupand/or relative maturity. In some examples, the area of adaptability mayinclude using soybean to produce a second crop during a growing season.Second crops are commonly planted in areas with longer growing seasons,however the selected crop may need different reproductivecharacteristics to be adapted for the second growing cycle in the seasonthan it would for the first growing cycle of the season. Any method ofenvironmental classification can be used, including but not limited tothose described in U.S. Pat. No. 8,032,389, and Loeffler et al. (2005)Crop Sci 45:1708-1716, each of which is herein incorporated by referencein its entirety. In certain examples, the marker profile comprises twoor more markers selected from the group consisting of S01435-1-001 on LGA1 (ch 5), S01239-1-A and/or S00780-1-A on LG A2 (ch 8), S06925-1-Q1,S09951-1-Q1, and/or S00170-1-A on LG B1 (ch 11), S04059-1-A and/orS07851-1-Q1 on LG B2 (ch 14), S11659-1-Q1, S04279-1-A, S02211-1-A,and/or S08942-1-Q1 on LG Cl (ch 4), S05742-1-Q1, S09155-1-Q1,S02037-1-A, S13136-1-Q1, S17291-001-K001, S13139-1-Q1, S17292-001-K001,S13146-1-Q1, S17293-001-K001, S17294-001-K001, S17581-001-Q008,S17691-001-Q001, S17701-001-Q001, S03703-1-Q1, S17297-001-K001,S17298-001-K001, S17299-001-K001, S17300-001-K001, S17306-001-K001,S17310-001-K001, S17311-001-K001, S17312-001-K001, S17312-001-K001,S17316-001-K001, S17317-001-K001, S17318-001-K001, S17322-001-K001,S17326-001-K001, S17327-001-K001, S17328-001-K001, S17329-001-K001,S10746-1-Q1, S17331-001-K001, S17332-001-K001, S17337-001-K001,S13093-1-Q1, S12211-1-Q1, S04555-1-Q1, and/or S17301-001-K001 on LG C2(ch 6), S08519-1-Q1 on LG D1a (ch 1), S12876-1-Q1, S05937-1-Q1,S08575-1-Q1, S08669-1-Q1, S11212-1-Q1, and/or S00543-1-A on LG D1b (ch2), S01452-1-A and/or S11993-1-Q2 on LG D2 (ch 17), S13446-1-Q1 on LGE(ch 15), S00252-1-A, S04060-1-A, S02664-1-A, and/or S00281-1-A on LGF(ch 13), S01109-1-Q002, S13844-1-Q1, S05058-1-Q1 and/or S04660-1-A on LGG (ch 18), S09955-1-Q1 on LG H (ch 12), S08034-1-Q1 and/or S10293-1-Q1on LG I (ch 20), S03813-1-A and/or S02042-1-A on LG J (ch 16),S16601-001-Q001, S01481-1-A, S11309-1-Q1, S11320-1-Q1, and/or S04040-1-Aon LGL (ch 19), S00863-1-A, S17151-001-K001, S17153-001-K001,S17154-001-K001, S17156-001-K001, S17159-001-K001, S08590-1-Q1,S17242-001-K001, S17166-001-Q006, S17167-001-Q007, S08539-1-Q1,S17178-001-K001, S17179-001-K001, S17180-001-K001, S17181-001-K001,S17182-001-K001, S17183-001-K001, S02780-1-Q1, S12107-1-Q1,S03624-1-Q001, S01953-1-A, S00111-1-A, S04180-1-A, and/or S01008-1-B onLG M (ch 7), S12861-1-Q1, S04966-1-Q1, and/or S12867-1-Q002 on LGN (ch3), and S10631-1-Q1, S01574-1-A, S16594-001-Q10, and/or S02777-1-A on LGO (ch 10), or any combination thereof. In further examples, the markerprofile comprises markers from the set of markers described in Tables26-46.

In other examples, the one or more marker locus detected comprises oneor more markers within a chromosome interval selected from the groupconsisting of an interval on linkage group A1 flanked by and includingSatt364 and BARC-020479-04637, an interval on linkage group A2 flankedby and including S01239-1 and S00780-1, an interval on linkage group B1flanked by and including S06925-1 and S00170-1, an interval on linkagegroup B2 flanked by and including S04059-1-A and S07851-1-Q1, aninterval on linkage group B2 flanked by and including BARC-052789-11619and BARC-013273-00464, an interval on linkage group C1 flanked by andincluding S11659-1 and S02211-1, an interval on linkage group C1 flankedby and including BARC-042189-08197 and BARC-019093-0331, an interval onlinkage group C1 flanked by and including S02211-1 and S08942-1, aninterval on linkage group C2 flanked by and including S05742-1 andBARCSOYSSR_06_0283, an interval on linkage group C2 flanked by andincluding S05742-1 and BARC-035239-07157, an interval on linkage groupC2 flanked by and including BARC-0299-06757 and Satt322, an interval onlinkage group C2 flanked by and including S13136-1 and S17294-001, aninterval on linkage group C2 flanked by and including S17297-001 andS17317-001, an interval on linkage group C2 flanked by and includingS17318-001 and S17331-001, an interval on linkage group D1a flanked byand including BARC-024147-04784 and BARC-045297-08928, an interval onlinkage group D1b flanked by and including BARC-029753-06334 andBARC-013995-01298, an interval on linkage group D1b flanked by andincluding S12876-1 and S08575-1, an interval on linkage group D1bflanked by and including S08669-1 and S11212-1, an interval on linkagegroup D1b flanked by and including S08575-1 and S08669-1, an interval onlinkage group D2 flanked by and including Satt389 andBARC-040583-007786, an interval on linkage group D2 flanked by andincluding S01452-1 and S11993-1, an interval on linkage group E flankedby and including BARC-020425-04614 and Satt231, an interval on linkagegroup F flanked by and including S00252-1 and Sat 039, an interval onlinkage group F flanked by and including S04060-1 and S00281-1, aninterval on linkage group G flanked by and including BARC-020027-04405and Satt309, an interval on linkage group G flanked by and includingS13844-1 and BARC-013305-00475, an interval on linkage group G flankedby and including Sat 064 and BARC-013305-00475, an interval on linkagegroup H flanked by and including BARC-018437-03181 and Satt629, aninterval on linkage group I flanked by and including S08034-1 andS10293-1, an interval on linkage group I flanked by and includingS10293-1 and Satt299, an interval on linkage group J flanked by andincluding Sct_046 and Satt693, an interval on linkage group J flanked byand including Satt547 and BARC-030817-06946, an interval on linkagegroup M flanked by and including S00863-1 and S17167-001, an interval onlinkage group M flanked by and including BARCSOYSSR_07_0017 andS08590-1, an interval on linkage group M flanked by and includingS08590-1 and S17167-001, an interval on linkage group M flanked by andincluding S00111-1 and Sat_121, an interval on linkage group M flankedby and including S00111-1 and, and/or S01008-1, an interval on linkagegroup N flanked by and including Sat_236 and Satt339, an interval onlinkage group N flanked by and including S12862-1 and S12867-1, aninterval on linkage group N flanked by and including Sat_125 andBARC-039729-07559, and an interval on linkage group O flanked by andincluding S02777-1 and BARC-029629-06265, or any interval provided inTables 28-46.

In further examples, the one or more marker locus detected comprises oneor more markers within one or more of the genomic DNA regions of SEQ IDNOs: 1-512. In other examples, the one or more marker locus detectedcomprises one or more markers within one or more of the genomic regionsof SEQ ID NOs:5, 10, 15, 20, 25, 30, 35, 40, 45, S0, 55, 60, 65, 70, 75,80, 84, 89, 93, 98, 102, 106, 111, 115, 120, 125, 129, 133, 137, 141,145, 149, 153, 157, 161, 165, 169, 173, 177, 181, 185, 189, 193, 197,202, 206, 210, 214, 219, 224, 229, 234, 239, 244, 249, 254, 259, 264,269, 274, 279, 284, 289, 294, 299, 304, 309, 314, 319, 324, 329, 334,339, 344, 349, 354, 359, 364, 369, 374, 378, 382, 386, 390, 394, 399,403, 408, 413, 418, 422, 426, 430, 434, 438, 442, 447, 452, 457, 462,467, 472, 477, 482, 487, 492, 497, 502, 507, or, 512. In some examples,the one or more polymorphism detected may be less than 1 cM, 1 cM, 5 cM,10 cM, 15 cM, 20 cM, or 30 cM from SEQ ID NOs: 1-512. In furtherexamples, the one or more marker locus detected comprises one or moremarkers within a chromosome interval described in Tables 28-46.

In some examples, the method comprises detecting one or morepolymorphisms linked to one or more loci, said loci comprising apolymorphism selected from the group consisting of Gm05:30568085,Gm08:7464336, Gm08:15841570, Gm11:4674824, Gm11:5231500, Gm11:7847341,Gm14:46138053, Gm14:47331319, Gm04:5754268, Gm04:8295779, Gm04:39691731,Gm04:44725098, Gm06:410442, Gm06:11659627, Gm06:15457913, Gm06:16391391,Gm06:16499786, Gm06:16593381, Gm06:16670047, Gm06:16804435,Gm06:17498270, Gm06:18203964, Gm06:19743496, Gm06:19986645,Gm06:20007173, Gm06:20084642, Gm06:20501491, Gm06:21197184,Gm06:21500085, Gm06:22501610, Gm06:25700006, Gm06:28501458,Gm06:28671736, Gm06:29499523, Gm06:30203054, Gm06:31694650,Gm06:32503141, Gm06:33196184, Gm06:35509548, Gm06:37712913,Gm06:38467854, Gm06:39168136, Gm06:39533730, Gm06:40766974,Gm06:41476201, Gm06:42450296, Gm06:47500976, Gm06:47521797,Gm06:48475049, Gm06:49978151, Gm06:22700011, Gm01:759365, Gm02:4893148,Gm02:9714426, Gm02:11502780, Gm02:15446229, Gm02:33158449,Gm02:45776142, Gm17:16136646, Gm17:39804515, Gm15:50237460, Gm13:235439,Gm13:20365663, Gm13:20744030, Gm13:35174140, Gm18:305113, Gm18:58086324,Gm18:61591142, Gm18:61831970, Gm12:11512115, Gm20:39051858,Gm20:41216234, Gm16:4678569, Gm16:36524407, Gm19:47535046,Gm19:47826727, Gm19:48252040, Gm19:48638646, Gm19:50222676,Gm07:1141099, Gm07:1830296, Gm07:1923026, Gm07:2179883, Gm07:2310058,Gm07:2679749, Gm07:3009018, Gm07:4282676, Gm07:4319368, Gm07:4342479,Gm07:5576650, Gm07:6288899, Gm07:6340656, Gm07:6347675, Gm07:6614649,Gm07:6616695, Gm07:6623333, Gm07:6671535, Gm07:7096376, Gm07:7774056,Gm07:8674220, Gm07:35590550, Gm07:36459825, Gm07:36638366,Gm03:38491492, Gm03:39583405, Gm03:46209939, Gm10:43974548,Gm10:44725777, Gm10:44732850, Gm10:50495033, or any combination thereof.

In some examples, the method comprises detecting a haplotype or a markerprofile comprising two or more of the polymorphisms linked to markerloci, said loci comprising a polymorphism selected from the groupconsisting of Gm05:30568085, Gm08:7464336, Gm08:15841570, Gm11:4674824,Gm11:5231500, Gm11:7847341, Gm14:46138053, Gm14:47331319, Gm04:5754268,Gm04:8295779, Gm04:39691731, Gm04:44725098, Gm06:410442, Gm06:11659627,Gm06:15457913, Gm06:16391391, Gm06:16499786, Gm06:16593381,Gm06:16670047, Gm06:16804435, Gm06:17498270, Gm06:18203964,Gm06:19743496, Gm06:19986645, Gm06:20007173, Gm06:20084642,Gm06:20501491, Gm06:21197184, Gm06:21500085, Gm06:22501610,Gm06:25700006, Gm06:28501458, Gm06:28671736, Gm06:29499523,Gm06:30203054, Gm06:31694650, Gm06:32503141, Gm06:33196184,Gm06:35509548, Gm06:37712913, Gm06:38467854, Gm06:39168136,Gm06:39533730, Gm06:40766974, Gm06:41476201, Gm06:42450296,Gm06:47500976, Gm06:47521797, Gm06:48475049, Gm06:49978151,Gm06:22700011, Gm01:759365, Gm02:4893148, Gm02:9714426, Gm02:11502780,Gm02:15446229, Gm02:33158449, Gm02:45776142, Gm17:16136646,Gm17:39804515, Gm15:50237460, Gm13:235439, Gm13:20365663, Gm13:20744030,Gm13:35174140, Gm18:305113, Gm18:58086324, Gm18:61591142, Gm18:61831970,Gm12:11512115, Gm20:39051858, Gm20:41216234, Gm16:4678569,Gm16:36524407, Gm19:47535046, Gm19:47826727, Gm19:48252040,Gm19:48638646, Gm19:50222676, Gm07:1141099, Gm07:1830296, Gm07:1923026,Gm07:2179883, Gm07:2310058, Gm07:2679749, Gm07:3009018, Gm07:4282676,Gm07:4319368, Gm07:4342479, Gm07:5576650, Gm07:6288899, Gm07:6340656,Gm07:6347675, Gm07:6614649, Gm07:6616695, Gm07:6623333, Gm07:6671535,Gm07:7096376, Gm07:7774056, Gm07:8674220, Gm07:35590550, Gm07:36459825,Gm07:36638366, Gm03:38491492, Gm03:39583405, Gm03:46209939,Gm10:43974548, Gm10:44725777, Gm10:44732850, Gm10:50495033, or anycombination thereof. In other examples, the haplotype or marker profilecomprises two or more polymorphisms described in Tables 26-46. In someexamples, the haplotype or the marker profile may comprise a combinationof early alleles and late alleles.

In some examples, the at least one favorable allele of one or moremarker loci is selected from the group consisting of an allele of amarker provided in Table 24. In some examples, the at least onefavorable allele of one or more marker loci is selected from the groupconsisting of an early allele of a marker provided in Table 25, or anycombination thereof.

Detecting may comprise isolating nucleic acids, amplifying the markerlocus or a portion of the marker locus and detecting the resultingamplified marker amplicon. In particular examples, the amplifyingcomprises admixing an amplification primer or amplification primer pairand, optionally at least one nucleic acid probe, with a nucleic acidisolated from the first soybean plant or germplasm, wherein the primeror primer pair and optional probe is complementary or partiallycomplementary to at least a portion of the marker locus and is capableof initiating DNA polymerization by a DNA polymerase using the soybeannucleic acid as a template; and, extending the primer or primer pair ina DNA polymerization reaction comprising a DNA polymerase and a templatenucleic acid to generate at least one amplicon. In particular examples,the detection comprises real time PCR analysis.

In still further aspects, the information disclosed herein regardingmarker alleles, haplotypes, and/or marker profiles can be used to aid inthe creation and/or selection of breeding plants, lines, and populationsfor a preferred reproductive growth phenotype, including but not limitedto at least one or more of a preferred time to initiation of flowering,early flowering, relative maturity, and/or length of reproductivegrowth. Further, the marker alleles, haplotypes, and/or marker profilescan be used for use in introgression into elite soybean germplasm,exotic soybean germplasm, or any other soybean germplasm. In someexamples the marker alleles, haplotypes, and/or marker profiles can beused to aid in the creation and/or selection of breeding plants, lines,and populations for a preferred reproductive growth phenotype for aspecific area of adaptation or target environment. Also provided is amethod for introgressing a soybean QTL, marker, haplotype, and/or markerprofile associated with at least a preferred time or length of at leastone reproductive stage into soybean germplasm. Methods are providedwherein one or more loci, markers, haplotypes and/or marker profiles areused to create and/or select soybean plants having at a preferred timeor length of at least one reproductive stage. Plants so created andselected can be used in a soybean breeding program. Through the processof introgression, the QTL, marker, haplotype, and/or marker profileassociated with a preferred time or length of at least one reproductivestage, such as a preferred time to initiation of flowering, earlyflowering, and/or length of reproductive growth, is introduced fromplants identified using marker-assisted selection (MAS) to other plants.According to the method, agronomically desirable plants and seeds can beproduced containing the QTL, marker, haplotype, and/or marker profileassociated with a preferred time or length of at least one reproductivestage from germplasm containing the QTL, marker, haplotype, and/ormarker profile.

Also provided herein is a method for producing a soybean plant adaptedfor a preferred reproductive growth phenotype. First, donor soybeanplants for a parental line containing at least one preferredreproductive growth QTL, marker, haplotype and/or marker profile areselected. According to the method, selection can be accomplished via MASas explained herein. Selected plant material may represent, amongothers, an inbred line, a hybrid line, a heterogeneous population ofsoybean plants, or an individual plant. According to techniques wellknown in the art of plant breeding, this donor parental line is crossedwith a second parental line. In some examples, the second parental lineis a high yielding line. This cross produces a segregating plantpopulation composed of genetically heterogeneous plants. Plants of thesegregating plant population are screened for the tolerance QTL, marker,or haplotype. Further breeding may include, among other techniques,additional crosses with other lines, hybrids, backcrossing, orself-crossing. The result is a line of soybean plants that has apreferred reproductive growth phenotype and optionally also has otherdesirable traits from one or more other soybean lines.

Also provided is a method of soybean plant breeding comprising crossingat least two different soybean parent plants, wherein the parent soybeanplants differ in time to R1 reproductive stage, obtaining a populationof progeny soybean seed from said cross, genotyping the progeny soybeanseed with at least one genetic marker, and, selecting a subpopulationcomprising at least one soybean seed possessing a genotype for alteredtime to R1 reproductive stage, wherein the mean time to R1 reproductivestage of the selected subpopulation is altered as compared to the meantime to R1 reproductive stage of the non-selected progeny. In someexamples the mean time to R1 reproductive stage of the selectedsubpopulation of progeny is at least 3-7 days different, or at least 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, or more days different than the meantime to R1 reproductive stage of the non-selected progeny. In otherexamples the mean time to R1 reproductive stage of the selectedsubpopulation of progeny is at least 2, 3, 4, 5, 6, 7, or 8 daysdifferent than the mean time to R1 reproductive stage of thenon-selected progeny. In some examples, the two different soybean parentplants also differ by maturity. The maturity groups of the parent plantsmay differ by one or more maturity subgroups, by one or more maturitygroups, or by 1 or more days to maturity. In some examples the parentsdiffer in maturity by at least 10 days, between 10 days-20 days, between10 days-30 days, by at least 0.1, 0.2, 0.3. 0.4, 0.5, 0.6, 0.7, 0.8, or0.9 maturity subgroups, by at least 1, 2, 3. 4, 5, 6, 7, 8, 9, 10, 11,or 12 maturity groups. In some examples one parent is adapted for anorthern growing region, and the second parent is not adapted for anorthern growing region. In some examples the parent adapted for anorthern growing region comprises a better reproductive growth phenotypefor a northern growing region than the parent not adapted for a northerngrowing region. In some examples, the method further comprises obtainingprogeny better adapted for a northern growing region.

In some examples the methods include identifying trait loci in a mixeddefined plant population comprising multiple plant families (see, e.g.,U.S. Pat. No. 6,399,855, herein incorporated by reference in itsentirety). The method comprises quantifying a phenotypic trait acrosslines sampled from the population, identifying at least one geneticmarker associated with the phenotypic trait by screening a set ofmarkers and identifying the quantitative trait loci based on theassociation of the phenotypic trait and the genetic marker(s). In someexamples the plant population consists of diploid plants, either hybridor inbred. The phenotypic traits associated with the locus arequantitative such that a numerical value can be ascribed to the trait,and the association of the genetic loci and the phenotypic trait isdetermined through specified statistical models. In some examples thestatistical models are linear models with fixed effects and randomeffects. In a other examples the statistical model is a mixed effectsmodel.

Soybean plants, seeds, tissue cultures, variants and mutants having apreferred reproductive growth phenotype produced by the foregoingmethods are also provided. Soybean plants, seeds, tissue cultures,variants and mutants comprising one or more of the marker loci, one ormore of the favorable alleles, and/or one or more of the haplotypes andhaving a preferred reproductive growth phenotype are provided. Alsoprovided are isolated nucleic acids, kits, and systems useful for theidentification, prediction, and/or selection methods disclosed herein.

In some examples, the soybean plant, germplasm, plant part, or seedhaving a preferred reproductive growth phenotype further comprises oneor more other traits of interest including but not limited to improvedresistance to one or more ALS-inhibiting herbicides, ahydroxyphenylpyruvatedioxygenase inhibitor, a phosphanoglycine(including but not limited to a glyphosate), a sulfonamide, animidazolinone, a bialaphos, a phosphinothricin, a metribuzin, amesotrione, an isoxaflutole, an azafenidin, a butafenacil, a sulfosate,a glufosinate, a dicamba, a 2,4-D, and a protox inhibitor. In someexamples, resistance to the herbicidal formulation is conferred by atransgene. In some examples, the plant or germplasm further comprises atrait selected from the group consisting of drought tolerance, stresstolerance, disease resistance, herbicide resistance, enhanced yield,modified oil, modified protein, tolerance to chlorotic conditions, andinsect resistance, or any combination thereof. In some examples, thetrait is selected from the group consisting of brown stem rotresistance, charcoal rot drought complex resistance, Fusariumresistance, Phytophthora resistance, stem canker resistance, suddendeath syndrome resistance, Sclerotinia resistance, Cercosporaresistance, anthracnose resistance, target spot resistance, frogeye leafspot resistance, soybean cyst nematode resistance, root knot nematoderesistance, rust resistance, high oleic content, low linolenic content,aphid resistance, stink bug resistance, and iron chlorosis deficiencytolerance, or any combination thereof. In some examples, one or more ofthe traits is conferred by one or more transgenes, by one or more nativeloci, or any combination thereof.

In another example a method of producing a cleaned soybean seed isprovided, the method comprising cleaning a soybean seed having at leastone locus conferred a preferred reproductive growth phenotype isprovided. In some examples, the cleaned soybean seed has enhanced yieldcharacteristics when compared to a soybean seed which has not beencleaned. Cleaned soybean seed produced by the methods are also provided.

In another example a method of producing a treated soybean seed isprovided, the method comprising treating a soybean seed having at leastone locus conferred a preferred reproductive growth phenotype isprovided. In some examples, the seed treatment comprises a fungicide, aninsecticide, or any combination thereof. In some examples the seedtreatment comprises trifloxystrobin, metalaxyl, imidacloprid, Bacillusspp., and any combination thereof. In some examples the seed treatmentcomprises picoxystrobin, penthiopyrad, cyantraniliprole,chlorantraniliprole, and any combination thereof. In some examples, theseed treatment improves seed germination under normal and/or stressenvironments, early stand count, vigor, yield, root formation,nodulation, and any combination thereof when compared to a soybean seedwhich has not been treated. In some examples seed treatment reduces seeddust levels, insect damage, pathogen establishment and/or damage, plantvirus infection and/or damage, and any combination thereof. Treatedsoybean seed produced by the methods are also provided.

It is to be understood that this invention is not limited to particularembodiments, which can, of course, vary. It is also to be understoodthat the terminology used herein is for the purpose of describingparticular embodiments only, and is not intended to be limiting.Further, all publications referred to herein are incorporated byreference for the purpose cited to the same extent as if each wasspecifically and individually indicated to be incorporated by referenceherein.

As used in this specification and the appended claims, terms in thesingular and the singular forms “a,” “an,” and “the,” for example,include plural referents unless the content clearly dictates otherwise.Thus, for example, reference to “plant,” “the plant,” or “a plant” alsoincludes a plurality of plants; also, depending on the context, use ofthe term “plant” can also include genetically similar or identicalprogeny of that plant; use of the term “a nucleic acid” optionallyincludes, as a practical matter, many copies of that nucleic acidmolecule; similarly, the term “probe” optionally (and typically)encompasses many similar or identical probe molecules.

Additionally, as used herein, “comprising” is to be interpreted asspecifying the presence of the stated features, integers, steps, orcomponents as referred to, but does not preclude the presence oraddition of one or more features, integers, steps, or components, orgroups thereof. Thus, for example, a kit comprising one pair ofoligonucleotide primers may have two or more pairs of oligonucleotideprimers. Additionally, the term “comprising” is intended to includeexamples encompassed by the terms “consisting essentially of” and“consisting of.” Similarly, the term “consisting essentially of” isintended to include examples encompassed by the term “consisting of.”

Certain definitions used in the specification and claims are providedbelow. In order to provide a clear and consistent understanding of thespecification and claims, including the scope to be given such terms,the following definitions are provided:

“Allele” means any of one or more alternative forms of a geneticsequence. In a diploid cell or organism, the two alleles of a givensequence typically occupy corresponding loci on a pair of homologouschromosomes. With regard to a SNP marker, allele refers to the specificnucleotide base present at that SNP locus in that individual plant.

The term “amplifying” in the context of nucleic acid amplification isany process whereby additional copies of a selected nucleic acid (or atranscribed form thereof) are produced. An “amplicon” is an amplifiednucleic acid, e.g., a nucleic acid that is produced by amplifying atemplate nucleic acid by any available amplification method.

“Backcrossing” is a process in which a breeder crosses a progeny varietyback to one of the parental genotypes one or more times.

The term “chromosome segment” designates a contiguous linear span ofgenomic DNA that resides in planta on a single chromosome. “Chromosomeinterval” refers to a chromosome segment defined by specific flankingmarker loci.

“Cultivar” and “variety” are used synonymously and mean a group ofplants within a species (e.g., Glycine max) that share certain genetictraits that separate them from other possible varieties within thatspecies. Soybean cultivars are inbred lines produced after severalgenerations of self-pollinations. Individuals within a soybean cultivarare homogeneous, nearly genetically identical, with most loci in thehomozygous state.

An “elite line” is an agronomically superior line that has resulted frommany cycles of breeding and selection for superior agronomicperformance. Numerous elite lines are available and known to those ofskill in the art of soybean breeding.

An “elite population” is an assortment of elite individuals or linesthat can be used to represent the state of the art in terms ofagronomically superior genotypes of a given crop species, such assoybean.

An “exotic soybean strain” or an “exotic soybean germplasm” is a strainor germplasm derived from a soybean not belonging to an available elitesoybean line or strain of germplasm. In the context of a cross betweentwo soybean plants or strains of germplasm, an exotic germplasm is notclosely related by descent to the elite germplasm with which it iscrossed. Most commonly, the exotic germplasm is not derived from anyknown elite line of soybean, but rather is selected to introduce novelgenetic elements (typically novel alleles) into a breeding program.

A “genetic map” is a description of genetic association or linkagerelationships among loci on one or more chromosomes (or linkage groups)within a given species, generally depicted in a diagrammatic or tabularform.

“Genotype” refers to the genetic constitution of a cell or organism.

“Germplasm” means the genetic material that comprises the physicalfoundation of the hereditary qualities of an organism. As used herein,germplasm includes seeds and living tissue from which new plants may begrown; or, another plant part, such as leaf, stem, pollen, or cells,that may be cultured into a whole plant. Germplasm resources providesources of genetic traits used by plant breeders to improve commercialcultivars.

An individual is “homozygous” if the individual has only one type ofallele at a given locus (e.g., a diploid individual has a copy of thesame allele at a locus for each of two homologous chromosomes). Anindividual is “heterozygous” if more than one allele type is present ata given locus (e.g., a diploid individual with one copy each of twodifferent alleles). The term “homogeneity” indicates that members of agroup have the same genotype at one or more specific loci. In contrast,the term “heterogeneity” is used to indicate that individuals within thegroup differ in genotype at one or more specific loci.

“Introgression” means the entry or introduction of a gene, QTL, marker,haplotype, marker profile, trait, or trait locus from the genome of oneplant into the genome of another plant.

The terms “label” and “detectable label” refer to a molecule capable ofdetection. A detectable label can also include a combination of areporter and a quencher, such as are employed in FRET probes or TAQMAN®probes. The term “reporter” refers to a substance or a portion thereofthat is capable of exhibiting a detectable signal, which signal can besuppressed by a quencher. The detectable signal of the reporter is,e.g., fluorescence in the detectable range. The term “quencher” refersto a substance or portion thereof that is capable of suppressing,reducing, inhibiting, etc., the detectable signal produced by thereporter. As used herein, the terms “quenching” and “fluorescence energytransfer” refer to the process whereby, when a reporter and a quencherare in close proximity, and the reporter is excited by an energy source,a substantial portion of the energy of the excited state nonradiativelytransfers to the quencher where it either dissipates nonradiatively oris emitted at a different emission wavelength than that of the reporter.

A “line” or “strain” is a group of individuals of identical parentagethat are generally inbred to some degree and that are generallyhomozygous and homogeneous at most loci (isogenic or near isogenic). A“subline” refers to an inbred subset of descendents that are geneticallydistinct from other similarly inbred subsets descended from the sameprogenitor. Traditionally, a subline has been derived by inbreeding theseed from an individual soybean plant selected at the F3 to F5generation until the residual segregating loci are “fixed” or homozygousacross most or all loci. Commercial soybean varieties (or lines) aretypically produced by aggregating (“bulking”) the self-pollinatedprogeny of a single F3 to F5 plant from a controlled cross between twogenetically different parents. While the variety typically appearsuniform, the self-pollinating variety derived from the selected planteventually (e.g., F8) becomes a mixture of homozygous plants that canvary in genotype at any locus that was heterozygous in the originallyselected F3 to F5 plant. Marker-based sublines that differ from eachother based on qualitative polymorphism at the DNA level at one or morespecific marker loci are derived by genotyping a sample of seed derivedfrom individual self-pollinated progeny derived from a selected F3-F5plant. The seed sample can be genotyped directly as seed, or as planttissue grown from such a seed sample. Optionally, seed sharing a commongenotype at the specified locus (or loci) are bulked providing a sublinethat is genetically homogenous at identified loci important for a traitof interest (e.g., yield, tolerance, etc.).

“Linkage” refers to the tendency for alleles to segregate together moreoften than expected by chance if their transmission was independent.Typically, linkage refers to alleles on the same chromosome. Geneticrecombination occurs with an assumed random frequency over the entiregenome. Genetic maps are constructed by measuring the frequency ofrecombination between pairs of traits or markers, the lower thefrequency of recombination, the greater the degree of linkage.

“Linkage disequilibrium” is a non-random association of 2 or morealleles wherein the 2 or more alleles occur together at a greaterfrequency than expected from their individual frequencies.

“Linkage group” refers to traits or markers that co-segregate. A linkagegroup generally corresponds to a chromosomal region containing geneticmaterial that encodes the traits or markers.

“Locus” is a defined segment of DNA.

A “management zone” is any specific area within a field that responds tomanagement practices in a similar way. There are various criteria andways to create management zones, including but not limited to using soildata, climate information, geographic data, and/or crop information inconjunction with an algorithm to identify areas of a field that are mostsimilar. The computer can take thousands of numbers and find areas thatare alike, cluster them together, and generate a map. Different zonescan be defined by using different data inputs, but weighting inputsdifferently, by assigning different criteria, or by identifyingdifferent management practices of interest. For example a managementzone for irrigation is probably not identical to a management zone forweed management for the same field in the same year.

Management zones may also use the same inputs and criteria and yetdiffer across years.

A “map location,” a “map position,” or a “relative map position” is anassigned location on a genetic map relative to linked genetic markerswhere a specified marker can be found within a given species. Mappositions are generally provided in centimorgans (cM), unless otherwiseindicated, genetic positions provided are based on the Glycine maxconsensus map v 4.0 as provided by Hyten et al. (2010) Crop Sci50:960-968. A “physical position” or “physical location” is theposition, typically in nucleotide bases, of a particular nucleotide,such as a SNP nucleotide, on the chromosome. Unless otherwise indicated,the physical position within the soybean genome provided is based on theGlyma 1.0 genome sequence described in Schmutz et al. (2010) Nature463:178-183, available from the Phytozome website(phytozome-dot-net/soybean).

“Mapping” is the process of defining the association and relationshipsof loci through the use of genetic markers, populations segregating forthe markers, and standard genetic principles of recombination frequency.

“Marker” or “molecular marker” is a term used to denote a nucleic acidor amino acid sequence that is sufficiently unique to characterize aspecific locus on the genome. Any detectible polymorphic trait can beused as a marker so long as it is inherited differentially and exhibitsnon-random association with a phenotypic trait of interest.

“Marker assisted selection” refers to the process of selecting a desiredtrait or traits in a plant or plants by detecting one or more nucleicacids from the plant, where the nucleic acid is associated with orlinked to the desired trait, and then selecting the plant or germplasmpossessing those one or more nucleic acids.

“Maturity Group” is an agreed-on industry division of groups ofvarieties, based on the zones in which they are adapted primarilyaccording to day length and/or latitude. Soybean varieties are groupedinto 13 maturity groups, depending on the climate and latitude for whichthey are adapted. Soybean maturities are divided into relative maturitygroups (denoted as 000, 00, 0, I, II, III, IV, V, VI, VII, VIII, IX, X,or 000, 00, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10). These maturity groups aregiven numbers, with numbers 000, 00, 0 and 1 typically being adapted toCanada and the northern United States, groups VII, VIII and IX beinggrown in the southern regions, and Group X is tropical. Within amaturity group are sub-groups. A sub-group is a tenth of a relativematurity group (for example 1.3 would indicate a group 1 and subgroup3). Within narrow comparisons, the difference of a tenth of a relativematurity group equates very roughly to a day difference in maturity atharvest.

A “mixed defined plant population” refers to a plant populationcontaining many different families and lines of plants. Typically, thedefined plant population exhibits a quantitative variability for aphenotype that is of interest. “Multiple plant families” refers todifferent families of related plants within a population.

“Haplotype” refers to a combination of particular alleles present withina particular plant's genome at two or more linked marker loci, forinstance at two or more loci on a particular linkage group. Forinstance, in one example, two specific marker loci on LG A1 are used todefine a haplotype for a particular plant. In still further examples, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or morelinked marker loci are used to define a haplotype for a particularplant.

As used herein, a “marker profile” means a combination of particularalleles present within a particular plant's genome at two or more markerloci which are not linked, for instance two or more loci on two or moredifferent linkage groups or two or more chromosomes. For instance, inone example, one marker locus on LG A1 and a marker locus on anotherlinkage group are used to define a marker profile for a particularplant. In certain other examples a plant's marker profile comprises oneor more haplotypes. In some examples, the marker profile encompasses twoor more loci for the same trait, such as time to first flower. In otherexamples, the marker profile encompasses two or more loci associatedwith two or more traits of interest, such as time to first flower and asecond trait of interest.

The term “plant” includes reference to an immature or mature wholeplant, including a plant from which seed or grain or anthers have beenremoved. Seed or embryo that will produce the plant is also consideredto be the plant.

“Plant parts” means any portion or piece of a plant, including leaves,stems, buds, roots, root tips, anthers, seed, grain, embryo, pollen,ovules, flowers, cotyledons, hypocotyls, pods, flowers, shoots, stalks,tissues, tissue cultures, cells, and the like.

“Polymorphism” means a change or difference between two related nucleicacids. A “nucleotide polymorphism” refers to a nucleotide that isdifferent in one sequence when compared to a related sequence when thetwo nucleic acids are aligned for maximal correspondence.

“Polynucleotide,” “polynucleotide sequence,” “nucleic acid sequence,”“nucleic acid fragment,” and “oligonucleotide” are used interchangeablyherein to indicate a polymer of nucleotides that is single- ormulti-stranded, that optionally contains synthetic, non-natural, oraltered RNA or DNA nucleotide bases. A DNA polynucleotide may becomprised of one or more strands of cDNA, genomic DNA, synthetic DNA, ormixtures thereof.

“Primer” refers to an oligonucleotide which is capable of acting as apoint of initiation of nucleic acid synthesis or replication along acomplementary strand when placed under conditions in which synthesis ofa complementary strand is catalyzed by a polymerase. Typically, primersare about 10 to 30 nucleotides in length, but longer or shortersequences can be employed. Primers may be provided in double-strandedform, though the single-stranded form is more typically used. A primercan further contain a detectable label, for example a 5′ end label.

“Probe” refers to an oligonucleotide that is complementary (though notnecessarily fully complementary) to a polynucleotide of interest andforms a duplexed structure by hybridization with at least one strand ofthe polynucleotide of interest. Typically, probes are oligonucleotidesfrom 10 to 50 nucleotides in length, but longer or shorter sequences canbe employed. A probe can further contain a detectable label.

“Quantitative trait loci” or “QTL” refer to the genetic elementscontrolling a quantitative trait.

“Recombination frequency” is the frequency of a crossing over event(recombination) between two genetic loci. Recombination frequency can beobserved by following the segregation of markers and/or traits duringmeiosis.

“Reproductive stage” is a description of the characteristics associatedwith various phases of reproductive growth.

“R1” is the first reproductive stage when soybean begins to bloom byproducing the first flower.

“Time to R1 reproductive stage” is measured in days unless otherwisestated.

“Tolerance and “improved tolerance” are used interchangeably herein andrefer to any type of” increase in resistance or tolerance to, or anytype of decrease in susceptibility. A “tolerant plant” or “tolerantplant variety” need not possess absolute or complete tolerance. Instead,a “tolerant plant,” “tolerant plant variety,” or a plant or plantvariety with “improved tolerance” will have a level of resistance ortolerance which is higher than that of a comparable susceptible plant orvariety.

“Self-crossing” or “self-pollination” or “selfing” is a process throughwhich a breeder crosses a plant with itself; for example, asecond-generation hybrid F2 with itself to yield progeny designatedF2:3.

“SNP” or “single nucleotide polymorphism” means a sequence variationthat occurs when a single nucleotide (A, T, C, or G) in the genomesequence is altered or variable. “SNP markers” exist when SNPs aremapped to sites on the soybean genome.

The term “yield” refers to the productivity per unit area of aparticular plant product of commercial value. For example, yield ofsoybean is commonly measured in bushels of seed per acre or metric tonsof seed per hectare per season. Yield is affected by both genetic andenvironmental factors.

An “isolated” or “purified” polynucleotide or polypeptide, orbiologically active portion thereof, is substantially or essentiallyfree from components that normally accompany or interact with thepolynucleotide or polypeptide as found in its naturally occurringenvironment. Typically, an “isolated” polynucleotide is free ofsequences (optimally protein encoding sequences) that naturally flankthe polynucleotide (i.e., sequences located at the 5′ and 3′ ends of thepolynucleotide) in the genomic DNA of the organism from which thepolynucleotide is derived. For example, the isolated polynucleotide cancontain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kbof nucleotide sequence that naturally flank the polynucleotide ingenomic DNA of the cell from which the polynucleotide is derived. Apolypeptide that is substantially free of cellular material includespreparations of polypeptides having less than about 30%, 20%, 10%, 5%,or 1% (by dry weight) of contaminating protein, culture media, or otherchemical components.

Standard recombinant DNA and molecular cloning techniques used hereinare well known in the art and are described more fully in Sambrook etal. Molecular Cloning: A Laboratory Manual; Cold Spring HarborLaboratory Press: Cold Spring Harbor, 1989 (hereinafter “Sambrook”).

Soybean is a short-day crop and its development is largely determined byvariety-specific day length requirements that initiate floraldevelopment. In other words, as the days grow shorter soybean willflower and enter into reproductive development stages. Due to thisphotoperiod requirement, days from planting until maturity cannot beaccurately estimated for soybean due to variation in planting date andother environmental variations. After flowering, temperature drivesdevelopment and the days until maturity can be estimated. The number ofdays from floral initiation (R1) until physiological maturity (R7) isusually independent of variety, but will vary slightly from year to yeardue to temperature differences between years. Although most sensitive today length, soybean flowering will be delayed to some extent with laterplanting dates. However, later planted soybean initiates floweringduring a warmer time of the year; therefore, post-flower developmentspeeds up. The precise number of days from full flower (R2) until R7cannot be predicted, but fairly reliable estimates can be derived fromhistorical information (see, e.g., Holshouser (2010) “Days to SoybeanPhysiological Maturity,” Virginia Cooperative Extension, Bulletin3009-1459; and, Heatherly (2005) “Soybean maturity group, planting dateand development related,” Delta Farm Press, Oct. 14, 2005).

Soybean growth is often characterized as comprising two stages:vegetative growth and reproductive growth. The vegetative (V) stages arenumbered according to how many fully-developed trifoliate leaves arepresent. The reproductive (R) stages begin at flowering and include poddevelopment, seed development, and plant maturation. Soybean yield isimpacted by genetics and environment, and various management practicescan impact crop growth and yield in the context of the genetics of thecrop. These stages are well-characterized and known (see, e.g.,McWilliams et al. (1999) Soybean Growth & Management Quick Guide,A-1174, NDSU Extension Service), and summarized in the table below.

Vegetative Stages Reproductive Stages VE Emergence R1 beginning bloom,1^(st) flower VC Cotyledon Stage R2 full bloom, flower in top 2 nodes V11st trifoliate leaf R3 beginning pod, 3/16″ pod in top 4 nodes V2 2^(nd)trifoliate R4 full pod, ¾″ pod in top 4 nodes V3 3^(rd) trifoliate R5 ⅛″seed in top 4 nodes Vn nth trifoliate R6 full size seed in top 4 nodesV6 flowering should R7 beginning maturity, one mature pod start soon R8full maturity, 95% of pods are mature

The advent of molecular genetic markers has facilitated mapping andselection of agriculturally important traits in soybean. Markers tightlylinked to tolerance genes are an asset in the rapid identification oftolerant soybean lines on the basis of genotype by the use of markerassisted selection (MAS). Introgressing tolerance genes into a desiredcultivar would also be facilitated by using suitable markers.

Soybean cultivar development for preferred reproductive growth phenotypecan be performed using classical breeding methods or by using markerassisted selection (MAS). Genetic markers for maturity or flowering timehave been identified.

Provided are markers, haplotypes, and/or marker profiles associated witha preferred reproductive growth phenotype, as well as related primersand/or probes and methods for the use of any of the foregoing foridentifying and/or selecting soybean plants with preferred time tofloral initiation. A method for determining the presence or absence ofat least one allele of a particular marker or haplotype associated withfloral initiation comprises analyzing genomic DNA from a soybean plantor germplasm to determine if at least one, or a plurality, of suchmarkers is present or absent and if present, determining the allelicform of the marker(s). If a plurality of markers on a single linkagegroup are investigated, this information regarding the markers presentin the particular plant or germplasm can be used to determine ahaplotype for that plant/germplasm.

In certain examples, plants or germplasm are identified that have atleast one favorable allele, marker, and/or haplotype that positivelycorrelate a preferred reproductive growth phenotype. However, in otherexamples, it is useful to identify alleles, markers, and/or haplotypesthat negatively correlate with a preferred reproductive growthphenotype, for example to eliminate such plants or germplasm fromsubsequent rounds of breeding, or to use as controls or check. Soybeanplants, cells, seed, varieties, and/or germplasm having preferredreproductive growth phenotype are provided.

Any marker associated with a preferred reproductive growth phenotypelocus or QTL is useful. Further, any suitable type of marker can beused, including Restriction Fragment Length Polymorphisms (RFLPs),Single Sequence Repeats (SSRs), Target Region AmplificationPolymorphisms (TRAPs), Isozyme Electrophoresis, Randomly AmplifiedPolymorphic DNAs (RAPDs), Arbitrarily Primed Polymerase Chain Reaction(AP-PCR), DNA Amplification Fingerprinting (DAF), Sequence CharacterizedAmplified Regions (SCARs), Amplified Fragment Length Polymorphisms(AFLPs), and Single Nucleotide Polymorphisms (SNPs). Additionally, othertypes of molecular markers known in the art or phenotypic traits mayalso be used as markers in the methods.

Markers that map closer to a QTL are generally used over markers thatmap farther from such a QTL. Marker loci are especially useful when theyare closely linked to a locus associated with a preferred reproductivegrowth phenotype. Thus, in one example, marker loci display aninter-locus cross-over frequency of about 10% or less, about 9% or less,about 8% or less, about 7% or less, about 6% or less, about 5% or less,about 4% or less, about 3% or less, about 2% or less, about 1% or less,about 0.75% or less, about 0.5% or less, or about 0.25% or less with aQTL to which they are linked. Thus, the loci are separated from the QTLto which they are linked by about 10 cM, 9 cM, 8 cM, 7 cM, 6 cM, 5 cM, 4cM, 3 cM, 2 cM, 1 cM, 0.75 cM, 0.5 cM, or 0.25 cM or less.

In certain examples, multiple marker loci that collectively make up ahaplotype and/or a marker profile are investigated, for instance 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, or more marker loci.

In addition to the markers discussed herein, information regardinguseful soybean markers can be found, for example, on the USDA's Soybasewebsite, available at soybase.org. A number of soybean markers have beenmapped and linkage groups created, as described in Cregan et al. (1999)Crop Sci 39:1464-90, Choi et al. (2007) Genetics 176:685-96, and Hyten,et al. (2010) Crop Sci 50:960-968, each of which is herein incorporatedby reference in its entirety, including any supplemental materialsassociated with the publication. Many soybean markers are publiclyavailable at the USDA affiliated soybase website (at soybase-dot-org).One of skill in the art will recognize that the identification offavorable marker alleles may be germplasm-specific. One of skill willalso recognize that methods for identifying the favorable alleles areroutine and well known in the art, and furthermore, that theidentification and use of such favorable alleles is well within thescope of the invention.

The use of marker assisted selection (MAS) to select a soybean plant orgermplasm based upon detection of a particular marker or haplotype ofinterest is provided. For instance, in certain examples, a soybean plantor germplasm possessing a certain predetermined favorable marker alleleor haplotype will be selected via MAS. Using MAS, soybean plants orgermplasm can be selected for markers or marker alleles that positivelycorrelate with tolerance, without actually raising soybean and measuringfor tolerance (or, contrawise, soybean plants can be selected against ifthey possess markers that negatively correlate with tolerance). MAS is apowerful tool to select for desired phenotypes and for introgressingdesired traits into cultivars of soybean (e.g., introgressing desiredtraits into elite lines). MAS is easily adapted to high throughputmolecular analysis methods that can quickly screen large numbers ofplant or germplasm genetic material for the markers of interest and ismuch more cost effective than raising and observing plants for visibletraits.

In some examples, molecular markers are detected using a suitableamplification-based detection method. Typical amplification methodsinclude various polymerase based replication methods, including thepolymerase chain reaction (PCR), ligase mediated methods, such as theligase chain reaction (LCR), and RNA polymerase based amplification(e.g., by transcription) methods. In these types of methods, nucleicacid primers are typically hybridized to the conserved regions flankingthe polymorphic marker region. In certain methods, nucleic acid probesthat bind to the amplified region are also employed. In general,synthetic methods for making oligonucleotides, including primers andprobes, are well known in the art. For example, oligonucleotides can besynthesized chemically according to the solid phase phosphoramiditetriester method described by Beaucage & Caruthers (1981) TetrahedronLetts 22:1859-1862, e.g., using a commercially available automatedsynthesizer, e.g., as described in Needham-VanDevanter et al. (1984)Nucl Acids Res 12:6159-6168. Oligonucleotides, including modifiedoligonucleotides, can also be ordered from a variety of commercialsources known to persons of skill in the art.

It will be appreciated that suitable primers and probes to be used canbe designed using any suitable method. It is not intended that theinvention be limited to any particular primer, primer pair, or probe.For example, primers can be designed using any suitable softwareprogram, such as LASERGENE® or Primer3.

The primers are not limited to generating an amplicon of any particularsize. For example, the primers used to amplify the marker loci andalleles herein are not limited to amplifying the entire region of therelevant locus. In some examples, marker amplification produces anamplicon at least 20 nucleotides in length, or alternatively, at leastS0 nucleotides in length, or alternatively, at least 100 nucleotides inlength, or alternatively, at least 200 nucleotides in length, oralternatively, at least 300 nucleotides in length, or alternatively, atleast 400 nucleotides in length, or alternatively, at least S00nucleotides in length, or alternatively, at least 1000 nucleotides inlength, or alternatively, at least 2000 nucleotides in length or more.

PCR, RT-PCR, and LCR are common amplification andamplification-detection methods for amplifying nucleic acids of interest(e.g., those comprising marker loci), facilitating detection of themarkers. Details regarding the use of these and other amplificationmethods are well known in the art and can be found in any of a varietyof standard texts. Details for these techniques can also be found innumerous references, such as Mullis et al. (1987) U.S. Pat. No.4,683,202; Arnheim & Levinson (1990) C&EN 36-47; Kwoh et al. (1989) ProcNatl Acad Sci USA 86:1173; Guatelli et al. (1990) Proc Natl Acad Sci USA87:1874; Lomell et al. (1989) J Clin Chem 35:1826; Landegren et al.(1988) Science 241:1077-1080; Van Brunt (1990) Biotechnology 8:291-294;Wu & Wallace (1989) Gene 4:560; Barringer et al. (1990) Gene 89:117; andSooknanan & Malek (1995) Biotechnology 13:563-564.

Such nucleic acid amplification techniques can be applied to amplifyand/or detect nucleic acids of interest, such as nucleic acidscomprising marker loci.

Amplification primers for amplifying useful marker loci and suitableprobes to detect useful marker loci or to genotype alleles, such as SNPalleles, are provided. For example, exemplary primers and probes areprovided in Table 26. However, one of skill will immediately recognizethat other primer and probe sequences could also be used. For instance,primers to either side of the given primers can be used in place of thegiven primers, so long as the primers can amplify a region that includesthe allele to be detected, as can primers and probes directed to othermarker loci. Further, it will be appreciated that the precise probe tobe used for detection can vary, e.g., any probe that can identify theregion of a marker amplicon to be detected can be substituted for thoseexamples provided herein. Further, the configuration of theamplification primers and detection probes can, of course, vary. Thus,the compositions and methods are not limited to the primers and probesspecifically recited herein.

In certain examples, probes will possess a detectable label. Anysuitable label can be used with a probe. Detectable labels suitable foruse with nucleic acid probes include, for example, any compositiondetectable by spectroscopic, radioisotopic, photochemical, biochemical,immunochemical, electrical, optical, or chemical means. Useful labelsinclude biotin for staining with labeled streptavidin conjugate,magnetic beads, fluorescent dyes, radiolabels, enzymes, and colorimetriclabels. Other labels include ligands, which bind to antibodies labeledwith fluorophores, chemiluminescent agents, and enzymes. A probe canalso constitute radiolabelled PCR primers that are used to generate aradiolabelled amplicon. Labeling strategies for labeling nucleic acidsand their corresponding detection strategies can be found, e.g., inHaugland (1996) Handbook of Fluorescent Probes and Research ChemicalsSixth Edition by Molecular Probes, Inc. (Eugene, Oreg.); or Haugland(2001) Handbook of Fluorescent Probes and Research Chemicals EighthEdition by Molecular Probes, Inc. (Eugene, Oreg.).

Detectable labels may also include reporter-quencher pairs, such as areemployed in Molecular Beacon and TAQMAN® probes. The reporter may be afluorescent organic dye modified with a suitable linking group forattachment to the oligonucleotide, such as to the terminal 3′ carbon orterminal 5′ carbon. The quencher may also be an organic dye, which mayor may not be fluorescent. Generally, whether the quencher isfluorescent or simply releases the transferred energy from the reporterby nonradiative decay, the absorption band of the quencher should atleast substantially overlap the fluorescent emission band of thereporter to optimize the quenching. Non-fluorescent quenchers or darkquenchers typically function by absorbing energy from excited reporters,but do not release the energy radiatively.

Selection of appropriate reporter-quencher pairs for particular probesmay be undertaken in accordance with known techniques. Fluorescent anddark quenchers and their relevant optical properties from whichexemplary reporter-quencher pairs may be selected are listed anddescribed, for example, in Berlman, Handbook of Fluorescence Spectra ofAromatic Molecules, 2nd ed., Academic Press, New York, 1971, the contentof which is incorporated herein by reference. Examples of modifyingreporters and quenchers for covalent attachment via common reactivegroups that can be added to an oligonucleotide in the present inventionmay be found, for example, in Haugland (2001) Handbook of FluorescentProbes and Research Chemicals Eighth Edition by Molecular Probes, Inc.(Eugene, Oreg.), the content of which is incorporated herein byreference.

In certain examples, reporter-quencher pairs are selected from xanthenedyes including fluorescein and rhodamine dyes. Many suitable forms ofthese compounds are available commercially with substituents on thephenyl groups, which can be used as the site for bonding or as thebonding functionality for attachment to an oligonucleotide. Anotheruseful group of fluorescent compounds for use as reporters is thenaphthylamines, having an amino group in the alpha or beta position.Included among such naphthylamino compounds are1-dimethylaminonaphthyl-5 sulfonate, 1-anilino-8-naphthalene sulfonateand 2-p-touidinyl-6-naphthalene sulfonate. Other dyes include3-phenyl-7-isocyanatocoumarin; acridines such as9-isothiocyanatoacridine; N-(p-(2-benzoxazolyl)phenyl)maleimide;benzoxadiazoles; stilbenes; pyrenes and the like. In certain otherexamples, the reporters and quenchers are selected from fluorescein andrhodamine dyes. These dyes and appropriate linking methodologies forattachment to oligonucleotides are well known in the art.

Suitable examples of reporters may be selected from dyes such as SYBRgreen, 5-carboxyfluorescein (5-FAM™ available from Applied Biosystems ofFoster City, Calif.), 6-carboxyfluorescein (6-FAM),tetrachloro-6-carboxyfluorescein (TET),2,7-dimethoxy-4,5-dichloro-6-carboxyfluorescein,hexachloro-6-carboxyfluorescein (HEX),6-carboxy-2′,4,7,7′-tetrachlorofluorescein (6-TET™ available fromApplied Biosystems), carboxy-X-rhodamine (ROX),6-carboxy-4′,5′-dichloro-2′,7′-dimethoxyfluorescein (6-JOE™ availablefrom Applied Biosystems), VIC™ dye products available from MolecularProbes, Inc., NED™ dye products available from available from AppliedBiosystems, and the like. Suitable examples of quenchers may be selectedfrom 6-carboxy-tetramethyl-rhodamine, 4-(4-dimethylaminophenylazo)benzoic acid (DABYL), tetramethylrhodamine (TAMRA), BHQ-0™, BHQ-1™,BHQ-2™, and BHQ-3™, each of which are available from BiosearchTechnologies, Inc. of Novato, Calif., QSY-7™, QSY-9™, QSY-21™ andQSY-35™, each of which are available from Molecular Probes, Inc., andthe like.

In one aspect, real time PCR or LCR is performed on the amplificationmixtures described herein, e.g., using molecular beacons or TAQMAN®probes. A molecular beacon (MB) is an oligonucleotide that, underappropriate hybridization conditions, self-hybridizes to form a stem andloop structure. The MB has a label and a quencher at the termini of theoligonucleotide; thus, under conditions that permit intra-molecularhybridization, the label is typically quenched (or at least altered inits fluorescence) by the quencher. Under conditions where the MB doesnot display intra-molecular hybridization (e.g., when bound to a targetnucleic acid, such as to a region of an amplicon during amplification),the MB label is unquenched. Details regarding standard methods of makingand using MBs are well established in the literature and MBs areavailable from a number of commercial reagent sources. See also, e.g.,Leone et al. (1995) Nucl Acids Res 26:2150-2155; Tyagi & Kramer (1996)Nat Biotechnol 14:303-308; Blok & Kramer (1997) Mol Cell Probes11:187-194; Hsuih et al. (1997) J Clin Microbiol 34:501-507; Kostrikiset al. (1998) Science 279:1228-1229; Sokol et al. (1998) Proc Natl AcadSci USA 95:11538-11543; Tyagi et al. (1998) Nat Biotechnol 16:49-53;Bonnet et al. (1999) Proc Natl Acad Sci USA 96:6171-6176; Fang et al.(1999) J Am Chem Soc 121:2921-2922; Marras et al. (1999) Genet AnalBiomol Eng 14:151-156; and, Vet et al. (1999) Proc Natl Acad Sci USA96:6394-6399. Additional details regarding MB construction and use arealso found in the patent literature, e.g., U.S. Pat. Nos. 5,925,517;6,150,097; and 6,037,130.

Another real-time detection method is the 5′-exonuclease detectionmethod, also called the TAQMAN® assay, as set forth in U.S. Pat. Nos.5,804,375; 5,538,848; 5,487,972; and 5,210,015, each of which is herebyincorporated by reference in its entirety. In the TAQMAN® assay, amodified probe, typically 10-30 nucleotides in length, is employedduring PCR which binds intermediate to or between the two members of theamplification primer pair. The modified probe possesses a reporter and aquencher and is designed to generate a detectable signal to indicatethat it has hybridized with the target nucleic acid sequence during PCR.As long as both the reporter and the quencher are on the probe, thequencher stops the reporter from emitting a detectable signal. However,as the polymerase extends the primer during amplification, the intrinsic5′ to 3′ nuclease activity of the polymerase degrades the probe,separating the reporter from the quencher, and enabling the detectablesignal to be emitted. Generally, the amount of detectable signalgenerated during the amplification cycle is proportional to the amountof product generated in each cycle.

It is well known that the efficiency of quenching is a strong functionof the proximity of the reporter and the quencher, i.e., as the twomolecules get closer, the quenching efficiency increases. As quenchingis strongly dependent on the physical proximity of the reporter andquencher, the reporter and the quencher are typically attached to theprobe within a few nucleotides of one another, usually within 30nucleotides of one another, or within 6 to 16 nucleotides. Typically,this separation is achieved by attaching one member of areporter-quencher pair to the 5′ end of the probe and the other memberto a nucleotide about 6 to 16 nucleotides away, in some cases at the 3′end of the probe.

Separate detection probes can also be omitted in amplification/detectionmethods, e.g., by performing a real time amplification reaction thatdetects product formation by modification of the relevant amplificationprimer upon incorporation into a product, incorporation of labelednucleotides into an amplicon, or by monitoring changes in molecularrotation properties of amplicons as compared to unamplified precursors(e.g., by fluorescence polarization).

One example of a suitable real-time detection technique that does notuse a separate probe that binds intermediate to the two primers is theKASPar detection system/method, which is well known in the art. InKASPar, two allele specific primers are designed such that the 3′nucleotide of each primer hybridizes to the polymorphic base. Forexample, if the SNP is an A/C polymorphism, one of the primers wouldhave an “A” in the 3′ position, while the other primer would have a “C”in the 3′ position. Each of these two allele specific primers also has aunique tail sequence on the 5′ end of the primer. A common reverseprimer is employed that amplifies in conjunction with either of the twoallele specific primers. Two 5′ fluor-labeled reporter oligos are alsoincluded in the reaction mix, one designed to interact with each of theunique tail sequences of the allele-specific primers. Lastly, onequencher oligo is included for each of the two reporter oligos, thequencher oligo being complementary to the reporter oligo and being ableto quench the fluor signal when bound to the reporter oligo. During PCR,the allele-specific primers and reverse primers bind to complementaryDNA, allowing amplification of the amplicon to take place. During asubsequent cycle, a complementary nucleic acid strand containing asequence complementary to the unique tail sequence of theallele-specific primer is created. In a further cycle, the reporteroligo interacts with this complementary tail sequence, acting as alabeled primer. Thus, the product created from this cycle of PCR is afluorescently-labeled nucleic acid strand. Because the labelincorporated into this amplification product is specific to the allelespecific primer that resulted in the amplification, detecting thespecific fluor presenting a signal can be used to determine the SNPallele that was present in the sample.

Further, it will be appreciated that amplification is not a requirementfor marker detection—for example, one can directly detect unamplifiedgenomic DNA simply by performing a Southern blot on a sample of genomicDNA. Procedures for performing Southern blotting, amplification e.g.,(PCR, LCR, or the like), and many other nucleic acid detection methodsare well established and are taught, e.g., in Sambrook et al. MolecularCloning—A Laboratory Manual (3d ed.) Vol. 1-3, Cold Spring HarborLaboratory, Cold Spring Harbor, N.Y., 2000 (“Sambrook”); CurrentProtocols in Molecular Biology, F. M. Ausubel et al., eds., CurrentProtocols, a joint venture between Greene Publishing Associates, Inc.and John Wiley & Sons, Inc., (supplemented through 2002) (“Ausubel”);and, PCR Protocols A Guide to Methods and Applications (Innis et al.,eds) Academic Press Inc. San Diego, Calif. (1990) (“Innis”). Additionaldetails regarding detection of nucleic acids in plants can also befound, e.g., in Plant Molecular Biology (1993) Croy (ed.) BIOSScientific Publishers, Inc.

Other techniques for detecting SNPs can also be employed, such as allelespecific hybridization (ASH) or nucleic acid sequencing techniques. ASHtechnology is based on the stable annealing of a short, single-stranded,oligonucleotide probe to a completely complementary single-strandedtarget nucleic acid. Detection is via an isotopic or non-isotopic labelattached to the probe. For each polymorphism, two or more different ASHprobes are designed to have identical DNA sequences except at thepolymorphic nucleotides. Each probe will have exact homology with oneallele sequence so that the range of probes can distinguish all theknown alternative allele sequences. Each probe is hybridized to thetarget DNA. With appropriate probe design and hybridization conditions,a single-base mismatch between the probe and target DNA will preventhybridization.

Isolated polynucleotide or fragments thereof are capable of specificallyhybridizing to other nucleic acid molecules under appropriateconditions. In one example, the nucleic acid molecules comprise any ofSEQ ID NOs: 1-512, complements thereof and fragments thereof. In anotheraspect, the nucleic acid molecules of the present invention includenucleic acid molecules that hybridize, for example, under high or lowstringency, substantially homologous sequences, or that have both tothese molecules. Conventional stringency conditions are described bySambrook et al. In: Molecular Cloning, A Laboratory Manual, 2nd Edition,Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (1989)), and byHaymes et al. In: Nucleic Acid Hybridization, A Practical Approach, IRLPress, Washington, D.C. (1985). Departures from complete complementarityare therefore permissible, as long as such departures do not completelypreclude the capacity of the molecules to form a double-strandedstructure. In order for a nucleic acid molecule to serve as a primer orprobe it need only be sufficiently complementary in sequence to be ableto form a stable double-stranded structure under the particular solventand salt concentrations employed. Appropriate stringency conditions thatpromote DNA hybridization are, for example, 6.0× sodium chloride/sodiumcitrate (SSC) at about 45° C., followed by a wash of 2.0×SSC at 50° C.,are known to those skilled in the art or can be found in CurrentProtocols in Molecular Biology, John Wiley & Sons, N.Y., 1989,6.3.1-6.3.6. For example, the salt concentration in the wash step can beselected from a low stringency of about 2.0×SSC at 50° C. to a highstringency of about 0.2×SSC at 50° C. In addition, the temperature inthe wash step can be increased from low stringency conditions at roomtemperature, about 22° C., to high stringency conditions at about 65° C.Both temperature and salt may be varied, or either the temperature orthe salt concentration may be held constant while the other variable ischanged.

In some examples, an a marker locus will specifically hybridize to oneor more of the nucleic acid molecules set forth in SEQ ID NOs: 1-512 orcomplements thereof or fragments of either under moderately stringentconditions, for example at about 2.0×SSC and about 65° C. In an aspect,a nucleic acid of the present invention will specifically hybridize toone or more SEQ ID NOs: 1-512 or complements or fragments of eitherunder high stringency conditions.

In some examples, a marker associated with a preferred reproductivegrowth phenotype comprises any one of SEQ ID NOs: 1-512 or complementsor fragments thereof. In other examples, a marker has between 80%, 85%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequenceidentity to any one of SEQ ID NOs: 1-512 or complements or fragmentsthereof. Unless otherwise stated, percent sequence identity isdetermined using the GAP program is default parameters for nucleic acidalignment (Accelrys, San Diego, Calif., USA).

Traits or markers are considered herein to be linked if they generallyco-segregate. A 1/100 probability of recombination per generation isdefined as a map distance of 1.0 centiMorgan (1.0 cM). The geneticelements or genes located on a single chromosome segment are physicallylinked. In some embodiments, the two loci are located in close proximitysuch that recombination between homologous chromosome pairs does notoccur between the two loci during meiosis with high frequency, e.g.,such that linked loci co-segregate at least about 90% of the time, e.g.,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.75%, or more ofthe time. The genetic elements located within a chromosome segment arealso genetically linked, typically within a genetic recombinationdistance of less than or equal to 50 centimorgans (cM), e.g., about 49,40, 30, 20, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0.75, 0.5, or 0.25 cM orless. That is, two genetic elements within a single chromosome segmentundergo recombination during meiosis with each other at a frequency ofless than or equal to about 50%, e.g., about 49%, 40%, 30%, 20%, 10%,9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.75%, 0.5%, or 0.25% or less.Closely linked markers display a cross over frequency with a givenmarker of about 10% or less (the given marker is within about 10 cM of aclosely linked marker). Put another way, closely linked locico-segregate at least about 90% of the time. With regard to physicalposition on a chromosome, closely linked markers can be separated, forexample, by about 1 megabase (Mb; 1 million nucleotides), about 500kilobases (Kb; 1000 nucleotides), about 400 Kb, about 300 Kb, about 200Kb, about 100 Kb, about 50 Kb, about 25 Kb, about 10 Kb, about 5 Kb,about 4 Kb, about 3 Kb, about 2 Kb, about 1 Kb, about 500 nucleotides,about 250 nucleotides, or less.

When referring to the relationship between two genetic elements, such asa genetic element contributing to tolerance and a proximal marker,“coupling” phase linkage indicates the state where the “favorable”allele at the tolerance locus is physically associated on the samechromosome strand as the “favorable” allele of the respective linkedmarker locus. In coupling phase, both favorable alleles are inheritedtogether by progeny that inherit that chromosome strand. In “repulsion”phase linkage, the “favorable” allele at the locus of interest (e.g., aQTL for tolerance) is physically linked with an “unfavorable” allele atthe proximal marker locus, and the two “favorable” alleles are notinherited together (i.e., the two loci are “out of phase” with eachother).

Markers are used to define a specific locus on the soybean genome. Eachmarker is therefore an indicator of a specific segment of DNA, having aunique nucleotide sequence. Map positions provide a measure of therelative positions of particular markers with respect to one another.When a trait is stated to be linked to a given marker it will beunderstood that the actual DNA segment whose sequence affects the traitgenerally co-segregates with the marker. More precise and definitelocalization of a trait can be obtained if markers are identified onboth sides of the trait. By measuring the appearance of the marker(s) inprogeny of crosses, the existence of the trait can be detected byrelatively simple molecular tests without actually evaluating theappearance of the trait itself, which can be difficult andtime-consuming because the actual evaluation of the trait requiresgrowing plants to a stage and/or under environmental conditions wherethe trait can be expressed. Molecular markers have been widely used todetermine genetic composition in soybeans.

Favorable genotypes associated with at least trait of interest may beidentified by one or more methodologies. In some examples one or moremarkers are used, including but not limited to AFLPs, RFLPs, ASH, SSRs,SNPs, indels, padlock probes, molecular inversion probes, microarrays,sequencing, and the like. In some methods, a target nucleic acid isamplified prior to hybridization with a probe. In other cases, thetarget nucleic acid is not amplified prior to hybridization, such asmethods using molecular inversion probes (see, for example Hardenbol etal. (2003) Nat Biotech 21:673-678). In some examples, the genotyperelated to a specific trait is monitored, while in other examples, agenome-wide evaluation including but not limited to one or more ofmarker panels, library screens, association studies, microarrays, genechips, expression studies, or sequencing such as whole-genomeresequencing and genotyping-by-sequencing (GBS) may be used. In someexamples, no target-specific probe is needed, for example by usingsequencing technologies, including but not limited to next-generationsequencing methods (see, for example, Metzker (2010) Nat Rev Genet11:31-46; and, Egan et al. (2012) Am J Bot 99:175-185) such assequencing by synthesis (e.g., Roche 454 pyrosequencing, Illumina GenomeAnalyzer, and Ion Torrent PGM or Proton systems), sequencing by ligation(e.g., SOLiD from Applied Biosystems, and Polnator system from AzcoBiotech), and single molecule sequencing (SMS or third-generationsequencing) which eliminate template amplification (e.g., Helicossystem, and PacBio RS system from Pacific BioSciences). Furthertechnologies include optical sequencing systems (e.g., Starlight fromLife Technologies), and nanopore sequencing (e.g., GridION from OxfordNanopore Technologies). Each of these may be coupled with one or moreenrichment strategies for organellar or nuclear genomes in order toreduce the complexity of the genome under investigation via PCR,hybridization, restriction enzyme (see, e.g., Elshire et al. (2011) PLoSONE 6:e19379), and expression methods. In some examples, no referencegenome sequence is needed in order to complete the analysis.

In some examples, markers within 1 cM, 5 cM, 10 cM, 15 cM, or 30 cM ofSEQ ID NO: 1-512 are provided. Similarly, one or more markers mappedwithin 1, 5, 10, 20 and 30 cM or less from the markers provided can beused for the selection or introgression of the region associated with apreferred reproductive growth phenotype. In other examples, any markerthat is linked with SEQ ID NOs: 1-512 and associated with a preferredreproductive growth phenotype is provided. In other examples, markersprovided include a substantially a nucleic acid molecule within 5 kb, 10kb, 20 kb, 30 kb, 100 kb, 500 kb, 1,000 kb, 10,000 kb, 25,000 kb, or50,000 kb of a marker selected from the group consisting of SEQ ID NOs:1-512.

Real-time amplification assays, including MB or TAQMAN® based assays,are especially useful for detecting SNP alleles. In such cases, probesare typically designed to bind to the amplicon region that includes theSNP locus, with one allele-specific probe being designed for eachpossible SNP allele. For instance, if there are two known SNP allelesfor a particular SNP locus, “A” or “C,” then one probe is designed withan “A” at the SNP position, while a separate probe is designed with a“C” at the SNP position. While the probes are typically identical to oneanother other than at the SNP position, they need not be. For instance,the two allele-specific probes could be shifted upstream or downstreamrelative to one another by one or more bases. However, if the probes arenot otherwise identical, they should be designed such that they bindwith approximately equal efficiencies, which can be accomplished bydesigning under a strict set of parameters that restrict the chemicalproperties of the probes. Further, a different detectable label, forinstance a different reporter-quencher pair, is typically employed oneach different allele-specific probe to permit differential detection ofeach probe. In certain examples, each allele-specific probe for acertain SNP locus is 13-18 nucleotides in length, dual-labeled with aflorescence quencher at the 3′ end and either the 6-FAM(6-carboxyfluorescein) or VIC(4,7,2′-trichloro-7′-phenyl-6-carboxyfluorescein) fluorophore at the 5′end.

To effectuate SNP allele detection, a real-time PCR reaction can beperformed using primers that amplify the region including the SNP locus,the reaction being performed in the presence of all allele-specificprobes for the given SNP locus. By then detecting signal for eachdetectable label employed and determining which detectable label(s)demonstrated an increased signal, a determination can be made of whichallele-specific probe(s) bound to the amplicon and, thus, which SNPallele(s) the amplicon possessed. For instance, when 6-FAM- andVIC-labeled probes are employed, the distinct emission wavelengths of6-FAM (518 nm) and VIC (554 nm) can be captured. A sample that ishomozygous for one allele will have fluorescence from only therespective 6-FAM or VIC fluorophore, while a sample that is heterozygousat the analyzed locus will have both 6-FAM and VIC fluorescence.

Introgression of a preferred reproductive growth phenotype into asoybean germplasm having an undesired or less preferred reproductivegrowth phenotype is provided. Any method for introgressing a QTL ormarker into soybean plants known to one of skill in the art can be used.Typically, a first soybean germplasm that contains a preferredreproductive growth phenotype derived from a particular marker orhaplotype and a second soybean germplasm that lacks such a reproductivegrowth phenotype derived from the marker or haplotype are provided. Thefirst soybean germplasm may be crossed with the second soybean germplasmto provide progeny soybean germplasm. These progeny germplasm arescreened to determine the presence a preferred reproductive growthphenotype derived from the marker or haplotype, and progeny that testspositive for the presence of tolerance derived from the marker orhaplotype are selected as being soybean germplasm into which the markeror haplotype has been introgressed. Methods for performing suchscreening are well known in the art and any suitable method can be used.

One application of MAS is to use the tolerance markers or haplotypes toincrease the efficiency of an introgression or backcrossing effort aimedat introducing a tolerance trait into a desired (typically highyielding) background. In marker assisted backcrossing of specificmarkers from a donor source, e.g., to an elite genetic background, oneselects among backcross progeny for the donor trait and then usesrepeated backcrossing to the elite line to reconstitute as much of theelite background's genome as possible.

Thus, the markers and methods can be utilized to guide marker assistedselection or breeding of soybean varieties with the desired complement(set) of allelic forms of chromosome segments associated with superioragronomic performance (tolerance, along with any other available markersfor yield, disease tolerance, etc.). Any of the disclosed marker allelesor haplotypes can be introduced into a soybean line via introgression,by traditional breeding (or introduced via transformation, or both) toyield a soybean plant with superior agronomic performance. The number ofalleles associated with tolerance that can be introduced or be presentin a soybean plant ranges from 1 to the number of alleles disclosedherein, each integer of which is incorporated herein as if explicitlyrecited.

This also provides a method of making a progeny soybean plant and theseprogeny soybean plants, per se. The method comprises crossing a firstparent soybean plant with a second soybean plant and growing the femalesoybean plant under plant growth conditions to yield soybean plantprogeny. Methods of crossing and growing soybean plants are well withinthe ability of those of ordinary skill in the art. Such soybean plantprogeny can be assayed for alleles associated with tolerance and,thereby, the desired progeny selected. Such progeny plants or seed canbe sold commercially for soybean production, used for food, processed toobtain a desired constituent of the soybean, or further utilized insubsequent rounds of breeding. At least one of the first or secondsoybean plants is a soybean plant that comprises at least one of themarkers or haplotypes associated with tolerance, such that the progenyare capable of inheriting the marker or haplotype.

Often, a method is applied to at least one related soybean plant such asfrom progenitor or descendant lines in the subject soybean plantspedigree such that inheritance of the desired tolerance can be traced.The number of generations separating the soybean plants being subject tothe methods will generally be from 1 to 20, commonly 1 to 5, andtypically 1, 2, or 3 generations of separation, and quite often a directdescendant or parent of the soybean plant will be subject to the method(i.e., 1 generation of separation).

Genetic diversity is important for long-term genetic gain in anybreeding program. With limited diversity, genetic gain will eventuallyplateau when all of the favorable alleles have been fixed within theelite population. One objective is to incorporate diversity into anelite pool without losing the genetic gain that has already been madeand with the minimum possible investment. MAS provides an indication ofwhich genomic regions and which favorable alleles from the originalancestors have been selected for and conserved over time, facilitatingefforts to incorporate favorable variation from exotic germplasm sources(parents that are unrelated to the elite gene pool) in the hopes offinding favorable alleles that do not currently exist in the elite genepool.

For example, the markers, haplotypes, primers, and probes can be usedfor MAS involving crosses of elite lines to exotic soybean lines (eliteX exotic) by subjecting the segregating progeny to MAS to maintain majoryield alleles, along with the tolerance marker alleles herein.

As an alternative to standard breeding methods of introducing traits ofinterest into soybean (e.g., introgression), transgenic approaches canalso be used to create transgenic plants with the desired traits. Inthese methods, exogenous nucleic acids that encode a desired QTL,marker, or haplotype are introduced into target plants or germplasm. Forexample, a nucleic acid that codes for a preferred reproductive growthtrait is cloned, e.g., via positional cloning, and introduced into atarget plant or germplasm.

Experienced plant breeders can recognize the time to R1 reproductivestage trait for soybean plants in the field, and can select theindividuals or populations for breeding purposes or for propagation withthe desired phenotype. In this context, the plant breeder recognizes“preferred” soybean plants. However, time to R1 is a phenotypic spectrumconsisting of extremes in timing, as well as a continuum of intermediatephenotypes. Evaluation of these intermediate phenotypes usingreproducible assays are of value to scientists who seek to identifygenetic loci that impart a specific time to R1 stage, to conduct markerassisted selection for populations, and to use introgression techniquesto breed a specific R1 trait into an elite soybean line, for example.

In some examples, a kit for detecting markers or haplotypes, and/or forcorrelating the markers or haplotypes with a desired phenotype (e.g., apreferred reproductive growth phenotype), are provided. Thus, a typicalkit can include a set of marker probes and/or primers configured todetect at least one favorable allele of one or more marker locusassociated with a preferred reproductive growth phenotype. These probesor primers can be configured, for example, to detect the marker allelesnoted in the tables and examples herein, e.g., using any availableallele detection format, such as solid or liquid phase array baseddetection, microfluidic-based sample detection, etc. The kits canfurther include packaging materials for packaging the probes, primers,or instructions; controls, such as control amplification reactions thatinclude probes, primers, and/or template nucleic acids foramplifications; molecular size markers; or the like.

System or kit instructions that describe how to use the system or kitand/or that correlate the presence or absence of the allele with thepredicted preferred or non-preferred phenotype are also provided. Forexample, the instructions can include at least one look-up table thatincludes a correlation between the presence or absence of the favorableallele(s) and the predicted time to floral initiation. The precise formof the instructions can vary depending on the components of the system,e.g., they can be present as system software in one or more integratedunit of the system (e.g., a microprocessor, computer or computerreadable medium), or can be present in one or more units (e.g.,computers or computer readable media) operably coupled to the detector.

Isolated nucleic acids comprising a nucleic acid sequence coding for apreferred reproductive growth phenotype, or capable of detecting such aphenotypic trait, or sequences complementary thereto, are also included.In certain examples, the isolated nucleic acids are capable ofhybridizing under stringent conditions to nucleic acids of a soybeancultivar phenotyped for a preferred reproductive growth phenotype, todetect loci associated with a preferred reproductive growth phenotype,including one or more of S01435-1, S01239-1, S00780-1, S06925-1,S09951-1, S00170-1, S04059-1, S07851-1, S11659-1, S04279-1, S02211-1,S08942-1, S05742-1, S09155-1, S02037-1, S13136-1, S17291-001, S13139-1,S17292-001, S13146-1, S17293-001, S17294-001, S17581-001, S17691-001,S17701-001, S03703-1, S17297-001, S17298-001, S17299-001, S17300-001,S17306-001, S17310-001, S17311-001, S17312-001, S17312-001, S17316-001,S17317-001, S17318-001, S17322-001, S17326-001, S17327-001, S17328-001,S17329-001, S10746-1, S17331-001, S17332-001, S17337-001, S13093-1,S12211-1, S04555-1, S17301-001, S08519-1, S12876-1, S05937-1, S08575-1,S08669-1, S11212-1, S00543-1, S01452-1, S11993-1, S13446-1, S00252-1,S04060-1, S02664-1, S00281-1, S01109-1, S13844-1, S05058-1, S04660-1,S09955-1, S08034-1, S10293-1, S03813-1, S02042-1, S16601-001, S01481-1,S11309-1, S11320-1, S04040-1, S00863-1, S17151-001, S17153-001,S17154-001, S17156-001, S17159-001, S08590-1, S17242-001, S17166-001,S17167-001, S08539-1, S17178-001, S17179-001, S17180-001, S17181-001,S17182-001, S17183-001, S02780-1, S12107-1, S03624-1, S01953-1,S00111-1, S04180-1, S01008-1, S12861-1, S04966-1, S12867-1, S10631-1-Q1,S01574-1, S16594-001, S02777-1, Gm05:30568085, Gm08:7464336,Gm08:15841570, Gm11:4674824, Gm11:5231500, Gm11:7847341, Gm14:46138053,Gm14:47331319, Gm04:5754268, Gm04:8295779, Gm04:39691731, Gm04:44725098,Gm06:410442, Gm06:11659627, Gm06:15457913, Gm06:16391391, Gm06:16499786,Gm06:16593381, Gm06:16670047, Gm06:16804435, Gm06:17498270,Gm06:18203964, Gm06:19743496, Gm06:19986645, Gm06:20007173,Gm06:20084642, Gm06:20501491, Gm06:21197184, Gm06:21500085,Gm06:22501610, Gm06:25700006, Gm06:28501458, Gm06:28671736,Gm06:29499523, Gm06:30203054, Gm06:31694650, Gm06:32503141,Gm06:33196184, Gm06:35509548, Gm06:37712913, Gm06:38467854,Gm06:39168136, Gm06:39533730, Gm06:40766974, Gm06:41476201,Gm06:42450296, Gm06:47500976, Gm06:47521797, Gm06:48475049,Gm06:49978151, Gm06:22700011, Gm01:759365, Gm02:4893148, Gm02:9714426,Gm02:11502780, Gm02:15446229, Gm02:33158449, Gm02:45776142,Gm17:16136646, Gm17:39804515, Gm15:50237460, Gm13:235439, Gm13:20365663,Gm13:20744030, Gm13:35174140, Gm18:305113, Gm18:58086324, Gm18:61591142,Gm18:61831970, Gm12:11512115, Gm20:39051858, Gm20:41216234,Gm16:4678569, Gm16:36524407, Gm19:47535046, Gm19:47826727,Gm19:48252040, Gm19:48638646, Gm19:50222676, Gm07:1141099, Gm07:1830296,Gm07:1923026, Gm07:2179883, Gm07:2310058, Gm07:2679749, Gm07:3009018,Gm07:4282676, Gm07:4319368, Gm07:4342479, Gm07:5576650, Gm07:6288899,Gm07:6340656, Gm07:6347675, Gm07:6614649, Gm07:6616695, Gm07:6623333,Gm07:6671535, Gm07:7096376, Gm07:7774056, Gm07:8674220, Gm07:35590550,Gm07:36459825, Gm07:36638366, Gm03:38491492, Gm03:39583405,Gm03:46209939, Gm10:43974548, Gm10:44725777, Gm10:44732850,Gm10:50495033, and any combination thereof.

In some examples the isolated nucleic acids are markers, for examplemarkers selected from the group consisting of S01435-1-001, S01239-1-A,S00780-1-A, S06925-1-Q1, S09951-1-Q1, S00170-1-A, S04059-1-A, S07851-1,S11659-1-Q1, S04279-1-A, S02211-1-A, S08942-1-Q1, S05742-1-Q1,S09155-1-Q1, S02037-1-A, S13136-1-Q1, S17291-001-K001, S13139-1-Q1,S17292-001-K001, S13146-1-Q1, S17293-001-K001, S17294-001-K001,S07518-001-Q008, S17691-001-Q001, S17701-001-Q001, S03703-1-Q1,S17297-001-K001, S17298-001-K001, S17299-001-K001, S17300-001-K001,S17306-001-K001, S17310-001-K001, S17311-001-K001, S17312-001-K001,S17312-001-K001, S17316-001-K001, S17317-001-K001, S17318-001-K001,S17322-001-K001, S17326-001-K001, S17327-001-K001, S17328-001-K001,S17329-001-K001, S10746-1-Q1, S17331-001-K001, S17332-001-K001,S17337-001-K001, S13093-1-Q1, S12211-1-Q1, S04555-1-Q1, S17301-001-K001,S08519-1-Q1, S12876-1-Q1, S05937-1-Q1, S08575-1-Q1, S08669-1-Q1,S11212-1-Q1, S00543-1-A, S01452-1-A, S11993-1-Q2, S13446-1-Q1,S00252-1-A, S04060-1-A, S02664-1-A, S00281-1-A, S01109-1-Q002,S13844-1-Q1, S05058-1-Q1, S04660-1-A, S09955-1-Q1, S08034-1-Q1,S10293-1-Q1, S03813-1-A, S02042-1-A, S16601-001-Q001, S01481-1-A,S11309-1-Q1, S11320-1-Q1, S04040-1-A, S00863-1-A, S17151-001-K001,S17153-001-K001, S17154-001-K001, S17156-001-K001, S17159-001-K001,S08590-1-Q1, S17242-001-K001, S17166-001-Q006, S17167-001-Q007,S08539-1-Q1, S17178-001-K001, S17179-001-K001, S17180-001-K001,S17181-001-K001, S17182-001-K001, S17183-001-K001, S02780-1-Q1,S12107-1-Q1, S03624-1-Q001, S01953-1-A, S00111-1-A, S04180-1-A,S01008-1-B, S12861-1-Q1, S04966-1-Q1, S12867-1-Q002, S10631-1-Q1,S01574-1-A, S16594-001-Q10, and S02777-1-A. In some examples the nucleicacid is one of more polynucleotides selected from the group consistingof SEQ ID NOs: 1-512. Vectors comprising one or more of such nucleicacids, expression products of such vectors expressed in a hostcompatible therewith, antibodies to the expression product (bothpolyclonal and monoclonal), and antisense nucleic acids are alsoincluded. In some examples, one or more of these nucleic acids isprovided in a kit.

As the parental line having a preferred reproductive growth phenotype,any line known to the art or disclosed herein may be used. Also includedare soybean plants produced by any of the foregoing methods. Seed of asoybean germplasm produced by crossing a soybean variety having a markeror haplotype associated with time to R1 reproductive stage with asoybean variety lacking such marker or haplotype, and progeny thereof,is also included.

A soybean plant, germplasm, plant part, or seed further comprisingresistance to at least one herbicidal formulation is provided. Forexample, the herbicidal formulation can comprise a compound selectedfrom the group consisting of an ALS-inhibiting herbicide, a glyphosate,a hydroxyphenylpyruvatedioxygenase (HPPD) inhibitor, a sulfonamide, animidazolinone, a bialaphos, a phosphinothricin, a metribuzin, amesotrione, an isoxaflutole, an azafenidin, a butafenacil, a sulfosate,a glufosinate, a dicamba, a 2,4-D, and a protox inhibitor. In someexamples, resistance to the herbicidal formulation is conferred by atransgene.

Glyphosate resistance can be conferred from genes including but notlimited to EPSPS, GAT, GOX, and the like, such as described in U.S. Pat.Nos. 6,248,876; 5,627,061; 5,804,425; 5,633,435; 5,145,783; 4,971,908;5,312,910; 5,188,642; 4,940,835; 5,866,775; 6,225,114; 6,130,366;5,310,667; 4,535,060; 4,769,061; 5,633,448; 5,510,471; RE36,449;RE37,287 E; 5,491,288; 5,776,760; 5,463,175; 8,044,261; 7,527,955;7,666,643; 7,998,703; 7,951,995; 7,968,770; 8,088,972, 7,863,503; andUS20030083480; WO 97/04103; WO 00/66746; WO 01/66704; and WO 00/66747,which are each incorporated herein by reference in their entireties forall purposes. Additionally, glyphosate tolerant plants can be generatedthrough the selection of naturally occurring mutations that imparttolerance to glyphosate.

HPPD resistance can be conferred by genes including exemplary sequencesdisclosed in U.S. Pat. Nos. 6,245,968; 6,268,549; and 6,069,115; and WO99/23886, which are each incorporated herein by reference in theirentireties for all purposes. Mutant hydroxyphenylpyruvatedioxygenaseshaving this activity are also known. For further examples seeUS20110185444 and US20110185445.

Resistance to auxins, such as 2,4-D or dicamba, can be provided bypolynucleotides as described, for example, in WO2005/107437,US20070220629, and U.S. Pat. No. 7,838,733 and in Herman et al. (2005)J. Biol. Chem. 280:24759-24767, each which is herein incorporated byreference.

Resistance to PPO-inhibiting herbicides can be provided as described inU.S. Pat. Nos. 6,288,306; 6,282,837; and 5,767,373; and WO 01/12825,each of which is herein incorporated by reference. Plants containingsuch polynucleotides can exhibit improved tolerance to any of a varietyof herbicides which target the protox enzyme. Resistance can also beconferred as described in US20100186131; US20110185444; US20100024080,each of which is herein incorporated by reference.

The development of plants containing an exogenous phosphinothricinacetyltransferase which confers resistance to glufosinate, bialaphos, orphosphinothricin is described, for example, in U.S. Pat. Nos. 5,969,213;5,489,520; 5,550,318; 5,874,265; 5,919,675; 5,561,236; 5,648,477;5,646,024; 6,177,616; and 5,879,903, which are each incorporated hereinby reference in their entireties for all purposes. Mutantphosphinothricin acetyltransferase having this activity are also knownin the art.

In some examples, the plant or germplasm further comprises a traitselected from the group consisting of drought tolerance, stresstolerance, disease resistance, herbicide resistance, enhanced yield,modified oil, modified protein, tolerance to chlorotic conditions, andinsect resistance, or any combination thereof. In some examples, thetrait is selected from the group consisting of brown stem rotresistance, charcoal rot drought complex resistance, Fusariumresistance, Phytophthora resistance, stem canker resistance, suddendeath syndrome resistance, Sclerotinia resistance, Cercosporaresistance, anthracnose resistance, target spot resistance, frogeye leafspot resistance, soybean cyst nematode resistance, root knot nematoderesistance, rust resistance, high oleic content, low linolenic content,aphid resistance, stink bug resistance, and iron chlorosis deficiencytolerance, or any combination thereof. In some examples, one or more ofthe traits is conferred by one or more transgenes, by one or more nativeloci, or any combination thereof. Examples of markers and lociconferring improved iron chlorosis deficiency tolerance are disclosed inUS20110258743, U.S. Pat. Nos. 7,582,806, and 7,977,533, each of which isherein incorporated by reference. Various disease resistance loci andmarkers are disclosed, for example, in WO1999031964, U.S. Pat. Nos.5,948,953, 5,689,035, US20090170112, US20090172829, US20090172830,US20110271409, US20110145953, U.S. Pat. Nos. 7,642,403, 7,919,675,US20110131677, U.S. Pat. Nos. 7,767,882, 7,910,799, US20080263720, U.S.Pat. No. 7,507,874, US20040034890, US20110055960, US20110185448,US20110191893, US20120017339, U.S. Pat. Nos. 7,250,552, 7,595,432,7,790,949, 7,956,239, 7,968,763, each of which is herein incorporated byreference. Markers and loci conferring improved yield are provided, forexample, in U.S. Pat. No. 7,973,212 and WO2000018963, each of which isherein incorporated by reference. Markers and loci conferring improvedresistance to insects are disclosed in, for example, US20090049565, U.S.Pat. No. 7,781,648, US20100263085, U.S. Pat. Nos. 7,928,286, 7,994,389,and WO2011116131, each of which is herein incorporated by reference.Markers and loci for modified soybean oil content or composition aredisclosed in, for example, US20120028255 and US20110277173, each ofwhich is herein incorporated by reference. Methods and compositions tomodified soybean oil content are described in, for example,WO2008147935, U.S. Pat. Nos. 8,119,860; 8,119,784; 8,101,189; 8,058,517;8,049,062; 8,124,845, 7,790,959, 7,531,718, 7,504,563, and 6,949,698,each of which is herein incorporated by reference. Markers and lociconferring tolerance to nematodes are disclosed in, for example,US20090064354, US20090100537, US20110083234, US20060225150,US20110083224, U.S. Pat. Nos. 5,491,081, 6,162,967, 6,538,175,7,872,171, 6,096,944, and 6,300,541, each of which is hereinincorporated by reference. Resistance to nematodes may be conferredusing a transgenic approach as described, for example, in U.S. Pat. Nos.6,284,948 and 6,228,992, each of which is herein incorporated byreference. Plant phenotypes can be modified using isopentyl transferasepolynucleotides as described, for example, in U.S. Pat. Nos. 7,553,951and 7,893,236, each of which is herein incorporated by reference.

Soybean seeds, plants, and plant parts comprising a preferredreproductive growth phenotype may be cleaned and/or treated. Theresulting seeds, plants, or plant parts produced by the cleaning and/ortreating process(es) may exhibit enhanced yield characteristics.Enhanced yield characteristics can include one or more of the following:increased germination efficiency under normal and/or stress conditions,improved plant physiology, growth and/or development, such as water useefficiency, water retention efficiency, improved nitrogen use, enhancedcarbon assimilation, improved photosynthesis, and acceleratedmaturation, and improved disease and/or pathogen tolerance. Yieldcharacteristics can furthermore include enhanced plant architecture(under stress and non-stress conditions), including but not limited toearly flowering, flowering control for hybrid seed production, seedlingvigor, plant size, internode number and distance, root growth, seedsize, fruit size, pod size, pod or ear number, seed number per pod orear, seed mass, enhanced seed filling, reduced seed dispersal, reducedpod dehiscence and lodging resistance. Further yield characteristicsinclude seed composition, such as carbohydrate content, protein content,oil content and composition, nutritional value, reduction inanti-nutritional compounds, improved processability and better storagestability.

Cleaning a seed or seed cleaning refers to the removal of impurities anddebris material from the harvested seed. Material to be removed from theseed includes but is not limited to soil, and plant waste, pebbles, weedseeds, broken soybean seeds, fungi, bacteria, insect material, includinginsect eggs, larvae, and parts thereof, and any other pests that existwith the harvested crop. The terms cleaning a seed or seed cleaning alsorefer to the removal of any debris or low quality, infested, or infectedseeds and seeds of different species that are foreign to the sample.

Treating a seed or applying a treatment to a seed refers to theapplication of a composition to a seed as a coating or otherwise. Thecomposition may be applied to the seed in a seed treatment at any timefrom harvesting of the seed to sowing of the seed. The composition maybe applied using methods including but not limited to mixing in acontainer, mechanical application, tumbling, spraying, misting, andimmersion. Thus, the composition may be applied as a powder, acrystalline, a ready-to-use, a slurry, a mist, and/or a soak. For ageneral discussion of techniques used to apply fungicides to seeds, see“Seed Treatment,” 2d ed., (1986), edited by K A Jeffs (chapter 9),herein incorporated by reference in its entirety. The composition to beused as a seed treatment can comprise one or more of a pesticide, afungicide, an insecticide, a nematicide, an antimicrobial, an inoculant,a growth promoter, a polymer, a flow agent, a coating, or anycombination thereof. General classes or family of seed treatment agentsinclude triazoles, anilides, pyrazoles, carboxamides, succinatedehydrogenase inhibitors (SDHI), triazolinthiones, strobilurins, amides,and anthranilic diamides. In some examples, the seed treatment comprisestrifloxystrobin, azoxystrobin, metalaxyl, metalaxyl-m, mefenoxam,fludioxinil, imidacloprid, thiamethoxam, thiabendazole, ipconazole,penflufen, sedaxane, prothioconazole, picoxystrobin, penthiopyrad,pyraclastrobin, xemium, Rhizobia spp., Bradyrhizobium spp. (e.g., B.japonicum), Bacillus spp. (e.g., B. firmus, B. pumilus, B. subtilus),lipochitooligosaccharide, clothianidin, cyantraniliprole,chlorantraniliprole, abamectin, and any combination thereof. In someexamples the seed treatment comprises trifloxystrobin, metalaxyl,imidacloprid, Bacillus spp., and any combination thereof. In someexamples the seed treatment comprises picoxystrobin, penthiopyrad,cyantraniliprole, chlorantraniliprole, and any combination thereof. Insome examples, the seed treatment improves seed germination under normaland/or stress environments, early stand count, vigor, yield, rootformation, nodulation, and any combination thereof. In some examplesseed treatment reduces seed dust levels, insect damage, pathogenestablishment and/or damage, plant virus infection and/or damage, andany combination thereof.

The present invention is illustrated by the following examples. Theforegoing and following description of the present invention and thevarious examples are not intended to be limiting of the invention butrather are illustrative thereof. Hence, it will be understood that theinvention is not limited to the specific details of these examples.

EXAMPLES Example 1

An F5 mapping population from a cross of 90Y50 and 90Y41 was used toidentify loci associated with reproductive stage traits in soybean. Thepopulation consisted of 340 progeny phenotyped for physiologicalmaturity. A set of 141 markers expected to be polymorphic were selectedacross all 20 chromosomes, and the samples were genotyped. Eighty-threemarkers showed monomorphism in this population and were removed fromanalysis. A further 35 markers were removed based on severe segregationdistortion (p<0.001). The remaining 22 markers were used to construct alinkage map and perform QTL analysis using Map Manager QTX.b20 (Manly etal. (2001) Mammalian Genome 12:930-932; available online atmapmanager.org). The initial parameters were set at: Linkage Evaluation:Intercross; search criteria: p=1e⁻⁵; map function: Kosambi; and, crosstype: line cross. A 1000 permutation test was used to establish thethreshold for statistical significance (LOD ratio statistic—LRS). Thematernal alleles were assigned as “A”, and the paternal alleles as “B”,and the heterozygous as “H”, and the “Low Signal” and “Equivocal” as “-”(missing). Chi-square test was used for goodness of fit test. Onemarker, S00281-1-A on LG F (Gm13:35174140, 73.16 cM) showed significantassociation in the QTL analysis.

Genomic DNA was extracted from leaf tissue of each progeny using amodification of the CTAB (cetyltriethylammonium bromide, Sigma H5882)method described by Stacey & Isaac (Methods in Molecular Biology, Vol.28: Protocols for Nucleic Acid Analysis by Nonradioactive Probes, Ed:Isaac, Humana Press Inc, Totowa, N.J. 1994, Ch 2, pp. 9-15).Approximately 100-200 mg of tissue was ground into powder in liquidnitrogen and homogenised in 1 ml of CTAB extraction buffer (2% CTAB,0.02 M EDTA, 0.1 M Tris-Cl pH 8, 1.4 M NaCl, 25 mM DTT) for 30 min at65° C. Homogenised samples were cooled at room temperature for 15 minbefore a single protein extraction with approximately 1 ml 24:1 v/vchloroform:octanol was done. Samples were centrifuged for 7 min at13,000 rpm and the upper layer of supernatant was collected usingwide-mouthed pipette tips. DNA was precipitated from the supernatant byincubation in 95% ethanol on ice for 1 h. DNA threads are spooled onto aglass hook, washed in 75% ethanol containing 0.2 M sodium acetate for 10min, air-dried for 5 min and resuspended in TE buffer. Five μl RNAse Awas added to the samples and incubated at 37° C. for 1 hour.

Example 2

An F2 mapping population from a cross of 90A01 and 90Y41 comprising 227progeny that were segregating for flowering date and for maturity datewas used to identify loci associated with the R1 reproductive stagetrait in soybean. A set of 197 markers was used to genotype the samples.The F2 plant samples were genotyped, and 1-4 F3 plants were phenotypedfor each F2 genotyped plant. Flowering date and maturity date wererecorded, and converted to sequential numbering with the earliest dateassigned to equal 1. The replicates were averaged to produce onephenotypic score/genotyped plant.

Genomic DNA was extracted essentially as described by Truett et al.(2000 BioTechniques 29:52-54). The samples are prepared for extractionby adding 400 μl Extraction Buffer (25 mM NaOH, 0.2 mM disodium EDTA (pHnot adjusted, ˜pH 12)) to sample racks containing 1-2 leaf punches and astainless steel bb for grinding in each well. Each plate is heat-sealed,and ground in a Genogrinder. After grinding, the plate is heated at 94°C. for 70 minutes. The seal is removed and 400 μl of NeutralizationBuffer is added (40 mM Tris-HCl (pH not adjusted, ˜pH 5)). The plate issealed with a new foil seal and shaken to mix the solutions. The sealedplate is centrifuged for 10 minutes. The final DNA extract contains 20mM Tris-HCl, pH 8.1, and 0.1 mM EDTA and is ready for use in variousassays.

Map Manager QTX.b20 (Manly et al. (2001) Mammalian Genome 12:930-932;available online at mapmanager.org) was used to construct the linkagemap using the following settings: Linkage Evaluation: Intercross; searchcriteria: p=1e⁻⁵; map function: Kosambi; and, cross type: line cross.

Single marker analysis (SMA), composite interval mapping (CIM), andmultiple interval mapping (MIM) were executed using QTL Cartographer 2.5(Wang et al. (2011) Windows QTL Cartographer 2.5; Dept. of Statistics,North Carolina State University, Raleigh, N.C. Available online atstatgen.ncsu.edu/qticart/WQTLCart.htm). The standard CIM model andforward and backward regression method was used, and the LRS thresholdfor statistical significance to declare QTLs was determined by a 500permutation test. The initial MIM model was determined using the CIMresults and the threshold found by permutation test. The defaultcriteria were used to optimize QTL positions, verify QTL significance,and search for interactions.

While evaluating the genotype data, 27 markers were removed from theanalysis for failing one or more criteria. Markers were evaluated forsegregation distortion via distribution of chi test results, from this11 markers were identified as severely distorted (p<0.0001), but wereretained in the analysis. Genotypic data across each progeny indicatedno selfed plants within the population, and all progeny had greater than70% data return.

Phenotype data for the population was also evaluated, 7 progeny withhigh standard deviation between replications of phenotypic scores andone progeny that was an extreme outlier for maturity were removed fromthe analysis. The remaining 219 progeny showed a relatively normaldistribution for maturity, and a skewed distribution for flowering(skewed left).

Linkage groups were created using 159 non-distorted markers, resultingin 28 linkage groups with 7 markers remaining unlinked. Three distortedmarkers formed an additional linkage group and the remaining 8 distortedmarkers could not be distributed.

Single marker analysis of the flowering time phenotypic dataset foundhighly significant associations on LG C2 (ch 6) in an interval flankedby and including S02037-1-A and S13093-1-Q1 at 89.19-113.11 cM. Table 1summarizes data for markers found with an F test statistic (pr(F))<0.05level of significance.

TABLE 1 Position QTL Marker LG (ch) (cM) Effect Pr(F) R2 S09155-1-Q1 C2(6) 69.29 90Y41 0.02132 0.0236 S02037-1-A C2 (6) 89.19 90Y41 0.000000.2749 S13136-1-Q1 C2 (6) 96.04 90Y41 0.00000 0.3702 S13146-1-Q1 C2 (6)98.23 90Y41 0.00000 0.3749 S10746-1-Q1 C2 (6) 104.94 90Y41 0.000000.3108 S13093-1-Q1 C2 (6) 113.11 90Y41 0.00002 0.0752 S12211-1-Q1 C2 (6)116.04 90Y41 0.00088 0.0477 S04555-1-Q1 C2 (6) 132.43 90Y41 0.029680.0194 S08539-1-Q1 M (7) 36.74 90A01 0.00578 0.0416 S08590-1-Q1 M (7)19.96 90A01 0.02616 0.0224 S01239-1-A A2 (8) 40.49 90A01 004836 0.0188S08669-1-Q1 D1b (2) 76.53 90A01 0.02989 0.0215 S11212-1-Q1 D1b (2) 83.2890A01 0.01806 0.0244 S03813-1-A J (16) 30.57 90Y41 0.01707 0.0259S02042-1-A J (16) 85.53 90Y41 0.04332 0.0187 S12862-1-Q1 N (3) 53.5690Y41 0.01687 0.023 S12867-1-Q002 N (3) 58.35 90Y41 0.02117 0.0242S04966-1-Q1 N (3) 92.16 90Y41 0.02070 0.0213

Single marker analysis of the maturity time phenotypic dataset foundhighly significant associations on LG C2 (ch 6) in an interval flankedby and including S02037-1-A and S13093-1-Q1 at 89.19-113.11 cM.Additional significant associations were found on LG D1b (ch 2) in aninterval at about 29.48-34.18 cM which included S12876-1-Q1, LG F (ch13) at marker S00252-1-A (˜0 cM), LG L (ch 19) at marker S04040-1-A(˜100.89 cM), and LG M (ch 7) at S08539-1-Q1 at about 36.74 cM. Table 2summarizes data for these markers with an F test statistic (pr(F))<0.05level of significance.

TABLE 2 Position QTL Marker LG (ch) (cM) Effect Pr(F) R2 S05742-1-Q1 C2(6) 4.88 90Y41 0.01338 0.0279 S09155-1-Q1 C2 (6) 69.29 90Y41 0.012710.0273 S02037-1-A C2 (6) 89.19 90Y41 0.00000 0.2741 S13136-1-Q1 C2 (6)94.84 90Y41 0.00000 0.3837 S13146-1-Q1 C2 (6) 98.23 90Y41 0.00000 0.4036S10746-1-Q1 C2 (6) 104.94 90Y41 0.00000 0.3463 S13093-1-Q1 C2 (6) 113.1190Y41 0.00005 0.0692 S12211-1-Q1 C2 (6) 116.04 90Y41 0.00026 0.0614S04555-1-Q1 C2 (6) 132.43 90Y41 0.00801 0.0292 S08590-1-Q1 M (7) 19.9690A01 0.00108 0.0487 S12107-1-Q1 M (7) 43.16 90A01 0.02162 0.0187S08539-1-Q1 M (7) 36.74 90A01 0.00218 0.0558 S12876-1-Q1 D1b (2) 29.4890Y41 0.00014 0.0645 S08669-1-Q1 D1b (2) 76.53 90Y41 0.02810 0.022S00252-1-A F (13) 0 90Y41 0.00606 0.046 S04060-1-A F (13) 36.9 90Y410.01496 0.0372 S02664-1-A F (13) 36.96 90Y41 0.03657 0.0223 S11309-1-Q1L (19) 91.1 90A01 0.01827 0.0231 S04040-1-A L (19) 100.89 90A01 0.005430.0351 S05058-1-Q1 G (18) 105.85 90Y41 0.01395 0.0275 S01435-1-Q001 A1(5) 33.61 90Y41 0.04597 0.0182 S00780-1-A A2 (8) 76.47 90A01 0.042700.017 S11659-1-Q1 C1 (4) 29.24 90Y41 0.01646 0.0253 S04279-1-A C1 (4)45.75 90Y41 0.03048 0.0275 S02211-1-A C1 (4) 54.48 90Y41 0.02204 0.0242

Composite interval mapping also identified the markers on LG C2associated with flowering date and with maturity date, as well as themarkers on LG D1b and LG M associated with maturity date. Four QTLs wereidentified on LG C2 for flowering date using a 1-LOD interval. The peakmarkers spanned 69.29 cM to 104.94 cM, and percent variation explainedranged from 22.6% to 66%. The QTL effect was from 90Y41 for all fourQTLs. Table 3 summarizes the CIM analysis for flowering dateassociations on LG C2.

TABLE 3 Marker LG (ch) Position (cM) LOD R2 S09155-1-Q1 C2 (6) 69.2921.1 0.461 S02037-1-A C2 (6) 89.19 16.0 0.226 S13146-1-Q1 C2 (6) 98.2340.5 0.660 S10746-1-Q1 C2 (6) 104.94 22.0 0.414

QTLs for maturity were identified on LG C2, D1b, and M. The QTLidentified in this analysis on LG C2 was in about the same region as theloci found for flowering date, with a peak position at S13146-1-Q1(98.23 cM). The percent variation explained was 44.9% and the effect wasfrom 90Y41. QTLs were identified on LG D1b, including a peak atS05937-1-Q1 (48.44 cM). The percent variation explained was 4.6% and theeffects were from 90A01. A QTL was also found on LG M with a peak atS08590-1-Q1 (19.96 cM), which explained about 4.8% of the phenotypicvariation and the effect was from 90A01. Table 4 summarizes the CIManalysis for maturity date associations on these linkage groups.

TABLE 4 Marker LG (ch) Position (cM) LOD R2 S13146-1-Q1 C2 (6) 98.2331.5 0.449 S05937-1-Q1 D1b (2) 48.44 4.6 0.058 S08590-1-Q1 M (7) 19.964.2 0.048

Multiple interval mapping (MIM) was performed to better estimate thepercent variation explained by each QTL and to test for QTL interactionsfor flowering date. MIM results indicated three QTLs on LG C2,explaining a total of 87.1% of the phenotypic variation for floweringdate (Table 5). Three epistatic interactions (A=Additive; D=Dominance;AA=Additive by Additive; AD=Additive by Dominance) were also identified,accounting for an additional 9.2% of the variation (Table 6). Combined,96.3% of the phenotypic variation was explained by this model.

TABLE 5 Marker LG (ch) Position (cM) R2 S09155-1-Q1 C2 (6) 69.29 −0.071S02037-1-A C2 (6) 89.19 0.109 S13146-1-Q1 C2 (6) 98.23 0.833

TABLE 6 QTL1 QTL2 Type Effect R2 1 2 AA −1.503 0.050 1 2 AD 0.477 −0.0801 3 AD 0.066 0.123

Multiple interval mapping (MIM) was performed to better estimate thepercent variation explained by each QTL and to test for QTL interactionsfor maturity date. The four QTLs identified in the CIM analysisexplained a total of about 67.7% of the phenotypic variation using MIM.One dominant by dominant (DD) epistatic interaction was identifiedbetween S13146-1-Q1 on LG C2 and S05837-1-Q1 on LG D1b, explaining anadditional 2% of the variation. Results are summarized in Table 7.

TABLE 7 Marker LG (ch) Position (cM) R2 S13146-1-Q1 C2 (6) 98.23 0.479S12876-1-Q1 D1b (2) 29.48 0.105 S05937-1-Q1 D1b (2) 48.44 0.049S08590-1-Q1 M (7) 19.96 0.044

Example 3

Genome-wide analysis indicated a reproductive stage QTL related tomaturity on LG M in 8 different biparental crosses. KASPar markers weredesigned across the putative region and used to fine map the locus.Three F3 populations were selected, two populations from 92Y91 X 92Y60(designated as JB5341 and JB5386 respectively), and one population from92Y80 X 92Y60 (JB5333). A total of 33 KASPar markers were designed andused to assay all populations in a region between 1.83 Mbps and 6.63Mbps on LGM. Phenotype data comprised maturity scores.

Map Manager QTX.b20 (Manly et al. (2001) Mammalian Genome 12:930-932;available online at mapmanager.org) was used to construct the linkagemap using the following settings: Linkage Evaluation: Intercross; searchcriteria: p=1e⁻⁵; map function: Kosambi; and, cross type: line cross.

Single marker analysis (SMA) and composite interval mapping (CIM) weredone using QTL Cartographer 2.5 (Wang et al. (2011) Windows QTLCartographer 2.5; Dept. of Statistics, North Carolina State University,Raleigh, N.C. Available online atstatgen.ncsu.edu/qticart/WQTLCart.htm). The standard CIM model andforward and backward regression method was used, and the default LRSthreshold of 11.5 was used to declare QTLs statistically significant.

Genotyping results indicated that 9 KASPar markers were polymorphic forJB5341, 14 KASPar markers were polymorphic for JB5386, and 13 KASParmarkers were polymorphic for JB5333. Six markers from previous genomewide analysis were added to each job. A chi test was performed toidentify segregation distortion, and indicated that 5 markers wereseverely distorted in JB5341, 12 in JB5386, and 2 in JB5333. A total of48 progeny were missing phenotypic scores and another three were missingmore than 30% data for JB5341. Likewise, one progeny was missing aphenotypic score and two were missing more than 30% data for JB5386.These 54 progeny were removed from the analysis. The phenotypicdistribution for each population was essentially normal for eachpopulation, though some distortion was observed in JB5341 as notedearlier.

Linkage groups were created for each population, with 6 linkage groupsformed and 5 unlinked markers for JB5386, 4 linkage groups and 1unlinked marker for JB5341, and two linkage groups and 1 unlinked markerfor JB5333.

Single marker analysis indicated minor significance on LG M in JB5341and JB5386, with the highest associations at S17179-001-K001 (40.83 cM)(PVE=5.7%) and S17159-001-K001 (18.14 cM) (PVE=2.2%), respectively.Highly significant markers were found in JB5333 between S00863-1 (8.09cM) and S01953-1 (48.13 cM). The peak marker was S17167-001-K001 at31.99 cM, with an R2 value of 37.7%. Table 8 summarizes all markers onLG M significant by single marker analysis at a pr(F)<0.05 level.

TABLE 8 JB5341 JB5386 JB5333 Marker Position Pr(F) R2 Pr(F) R2 Pr(F) R2S00863-1 8.09 — — — — 0.00000 0.075 S17151-001-K001 11.64 0.02341 0.029— — 0.00000 0.110 S17153-001-K001 12.12 0.00452 0.051 0.03158 0.0210.00000 0.147 S17154-001-K001 13.97 0.02816 0.033 — — 0.00000 0.138S17156-001-K001 15.53 0.01732 0.037 0.03859 0.021 0.00000 0.147S17159-001-K001 18.14 0.00873 0.044 0.03687 0.022 0.00000 0.125S17166-001-K001 31.87 — — — — 0.00000 0.345 S17167-001-K001 31.99 — — —— 0.00000 0.377 S17178-001-K001 40.59 — — — — 0.00000 0.154S17179-001-K001 40.83 0.00285 0.057 — — 0.00000 0.166 S17180-001-K00140.85 — — — 0.00000 0.152 S17181-001-K001 41.66 0.00285 0.052 — —0.00000 0.141 S17182-001-K001 41.66 — — — — 0.00000 0.145S17183-001-K001 41.69 0.00285 0.057 — — 0.00000 0.144 S03624-1 45.020.00203 0.054 — — — — S00111-1 79.14 0.03238 0.029 — — — — S02780-141.85 — — — — 0.00000 0.125 S01953-1 48.13 — — — — 0.00000 0.068S04180-1 86.05 — — — — 0.00878 0.020

Composite interval mapping analysis did not find any QTL for populationsJB5341 or JB5386, however a QTL was found for population JB5333. Thepeak for the region was near S17167-001-K001 (31.99 cM) on LG M, withLOD=35.1. This locus explained 37.8% of the phenotypic variation. Theadditive effect indicated that early maturity was from parent 92Y60.

Example 4

Additional markers targeting a region on LG C2 were developed to probethe F2 population from 90A01/90Y41 (Example 3) and to fine map one ormore loci associated with flowering data or maturity. Additional markerswere developed based on KASPar technology and used to saturate theregion to further refine the locus.

Forty-seven KASPar markers were developed to target a region on LG C2spanning 16.5 Mbps to 47.5 Mbps. The genotypic data from these markerswas combined with the results from 13 markers on LG C2 from previousanalysis.

Map Manager QTX.b20 (Manly et al. (2001) Mammalian Genome 12:930-932;available online at mapmanager.org) was used to construct the linkagemap using the following settings: Linkage Evaluation: Intercross; searchcriteria: p=1e⁻⁵; map function: Kosambi; and, cross type: line cross.

Single marker analysis (SMA), composite interval mapping (CIM), andmultiple interval mapping (MIM) were done using QTL Cartographer 2.5(Wang et al. (2011) Windows QTL Cartographer 2.5; Dept. of Statistics,North Carolina State University, Raleigh, N.C. Available online atstatgen.ncsu.edu/qticart/WQTLCart.htm). The standard CIM model andforward and backward regression method was used, and the default LRSthreshold for statistical significance was used to declare QTLsstatistically significant. Window size and walk speed parameters wereadjusted to narrow the QTL peak. The initial MIM model was determinedusing the MIM forward search method. The default criteria were used tooptimize QTL positions, verify QTL significance, and search forinteractions.

Preliminary analysis of the marker genotype data indicated 11 markerswere missing more than 30% data, nine markers were monomorphic, and 2failed. There was also one progeny that was removed from analysis basedon missing more than 30% data.

Reviewing phenotype data showed seven progeny with exceptionally highstandard deviations between phenotype score replicants, additionally oneprogeny was an extreme outlier for maturity. These progeny were removedfrom the analysis and the phenotypic distributions for flowering timeand for maturity of the remaining 218 progeny evaluated. The phenotypicdistribution for maturity was essentially normal, while the distributionfor flowering time had some skewing to the left. Linkage analysis wasdone and one linkage group was formed comprising all 38 markers.

Single marker analysis of the flowering time data set showed highlysignificant associations in an interval flanked by and comprisingS02037-1-A (89.19 cM) and S13093-1-Q1 (113.11 cM) on LG C2, with R2values ranging from 7.5% to 44.5%. The peak marker in this region wasS17297-001-K001 at 102.43 cM. Table 9 summarizes all markers associatedwith flowering time at a pr(F)<10⁻⁵ level of significance.

TABLE 9 Marker Position (cM) QTL Donor Pr(F) R2 S02037-1-A 89.19 90Y410.00000 0.274 S13136-1-Q1 94.84 90Y41 0.00000 0.369 S17291-001-K00196.04 90Y41 0.00000 0.369 S17292-001-K001 97.84 90Y41 0.00000 0.353S13146-1-Q1 98.23 90Y41 0.00000 0.374 S17293-001-K001 100.29 90Y410.00000 0.405 S17294-001-K001 101.72 90Y41 0.00000 0.413 S17297-001-K001102.43 90Y41 0.00000 0.445 S17298-001-K001 102.71 90Y41 0.00000 0.426S17299-001-K001 102.83 90Y41 0.00000 0.418 S17300-001-K001 102.93 90Y410.00000 0.410 S17301-001-K001 102.97 90Y41 0.00000 0.412 S17306-001-K001103.29 90Y41 0.00000 0.419 S17310-001-K001 103.3 90Y41 0.00000 0.421S17311-001-K001 103.3 90Y41 0.00000 0.378 S17312-001-K001 103.3 90Y410.00000 0.377 S17313-001-K001 103.31 90Y41 0.00000 0.399 S17316-001-K001103.31 90Y41 0.00000 0.389 S17317-001-K001 103.31 90Y41 0.00000 0.203S17318-001-K001 103.32 90Y41 0.00000 0.405 S17322-001-K001 103.37 90Y410.00000 0.378 S17326-001-K001 103.79 90Y41 0.00000 0.372 S17327-001-K001104 90Y41 0.00000 0.376 S17328-001-K001 104.25 90Y41 0.00000 0.349S17329-001-K001 104.38 90Y41 0.00000 0.324 S10746-1-Q1 104.94 90Y410.00000 0.310 S17331-001-K001 105.8 90Y41 0.00000 0.347 S17332-001-K001106.19 90Y41 0.00000 0.347 S17337-001-K001 113.1 90Y41 0.00001 0.080S13093-1-Q1 113.11 90Y41 0.00001 0.075

Single marker analysis of the maturity data set showed highlysignificant associations in an interval flanked by and comprisingS02037-1-A (89.19 cM) and S13093-1-Q1 (113.11 cM) on LG C2, with R2values ranging from 7.0% to 49.7%. The peak marker in this region wasS17297-001-K001 at 102.43 cM. Table 10 summarizes all markers associatedwith maturity at a pr(F)<10⁻⁵ level of significance.

TABLE 10 Marker Position (cM) QTL Donor Pr(F) R2 S02037-1-A 89.19 90Y410.00000 0.243 S13136-1-Q1 94.84 90Y41 0.00000 0.379 S17291-001-K00196.04 90Y41 0.00000 0.379 S17292-001-K001 97.84 90Y41 0.00000 0.367S13146-1-Q1 98.23 90Y41 0.00000 0.399 S17293-001-K001 100.29 90Y410.00000 0.449 S17294-001-K001 101.72 90Y41 0.00000 0.470 S17297-001-K001102.43 90Y41 0.00000 0.497 S17298-001-K001 102.71 90Y41 0.00000 0.494S17299-001-K001 102.83 90Y41 0.00000 0.484 S17300-001-K001 102.93 90Y410.00000 0.475 S17301-001-K001 102.97 90Y41 0.00000 0.481 S17306-001-K001103.29 90Y41 0.00000 0.488 S17310-001-K001 103.3 90Y41 0.00000 0.474S17311-001-K001 103.3 90Y41 0.00000 0.449 S17312-001-K001 103.3 90Y410.00000 0.433 S17313-001-K001 103.31 90Y41 0.00000 0.452 S17316-001-K001103.31 90Y41 0.00000 0.430 S17317-001-K001 103.31 90Y41 0.00000 0.356S17318-001-K001 103.32 90Y41 0.00000 0.453 S17322-001-K001 103.37 90Y410.00000 0.428 S17326-001-K001 103.79 90Y41 0.00000 0.426 S17327-001-K001104 90Y41 0.00000 0.425 S17328-001-K001 104.25 90Y41 0.00000 0.384S17329-001-K001 104.38 90Y41 0.00000 0.372 S10746-1-Q1 104.94 90Y410.00000 0.342 S17331-001-K001 105.8 90Y41 0.00000 0.345 S17332-001-K001106.19 90Y41 0.00000 0.345 S17337-001-K001 113.1 90Y41 0.00003 0.083S13093-1-Q1 113.11 90Y41 0.00003 0.070

The initial composite interval mapping results for flowering date usingthe default settings showed 4 QTLs on LG C2 between about 89.19 cM and104.38 cM. In further analyses the window size was adjusted to 5 cM, andthen to 1 cM, to narrow down the probable location of the locus. Thefinal results indicate a QTL peak at marker S17297-001-K001 explaining26.4% of the phenotypic variation for flowering time. Early floweringdate was from parent 90A01. Table 11 summarizes the results of CIManalysis on LG C2.

TABLE 11 Window Peak Position LRS R2 10 cM S13146-1-Q1 98.23 161.0 0.5265 cM S17297-001-K001 102.43 102.9 0.264 1 cM S17297-001-K001 102.43102.9 0.264

The initial composite interval mapping results for maturity using thedefault settings showed 2 QTLs on LG C2. In further analyses the windowsize was adjusted to 5 cM, and then to 1 cM, which resulted in a singleQTL. The final results indicate a QTL peak at marker S17297-001-K001explaining 49.7% of the phenotypic variation for maturity. Earlymaturity date was from parent 90A01. Table 12 summarizes the results ofCIM analysis on LG C2.

TABLE 12 Window Peak Position LRS R2 10 cM S17297-001-K001 102.43 150.40.497 5 cM S17297-001-K001 102.43 150.4 0.497 1 cM S17297-001-K001102.43 150.4 0.497

Multiple interval mapping (MIM) was used to corroborate the resultsobtained from composite interval mapping. MIM results indicated a singleQTL on LG C2 with a peak near S17297-001-K001 for both flowering dateand for maturity. In the MIM analysis 54.4% of the phenotypic variationin flowering time, and 49.9% of the phenotypic variation in maturity wasexplained by this model.

Example 5

Populations were developed by crossing lines from maturity groups (MG) 0or 1 with lines from maturity groups 3 or 4, specifically 90Y20/94Y22,90Y90/93Y82, and 91Y20/93Y82. Plants from F2 seed and check lines wereleaf punched and genotyped with markers S01574-1-A (E2) and S01481-1-A(E3), these markers are in high linkage disequilibrium (LD) with thecausative mutation at each respective locus. The polymorphism detectedby marker S01574-1-A has allele C associated with early flowering andallele A associated with late flowering. The polymorphism detected bymarker S01481-1-A polymorphism has allele T associated with earlyflowering and allele G associated with late flowering.

F3 seed were harvested from selected plants from each population,planted in randomized plots, and phenotyped for flowering time andmaturity during the growing season. The genotyping and phenotyping datasample information is summarized in Table 13.

TABLE 13 Population 90Y20/94Y22 90Y90/93Y82 91Y20/93Y82 F2 plantsgenotyped 552 736 1104 F3 plants phenotyped 91 184 265

Genotyping data was grouped into one of eight classes depending on theallele identified by each marker, and whether both loci are consideredin the analysis, and then phenotypic data aggregated and analyzedaccordingly. The data is summarized in Table 14.

TABLE 14 Avg. Avg. Genotype Avg. #days #days Class #F2:3 #days toplanting flowering (E2/E3) Pedigree progeny flowering to maturity tomaturity Note Late/late 94Y22 — 49 NA NA Check Early/Early 90Y20/94Y2222 34 100 66 Progeny Early/Late 90Y20/94Y22 24 38 106 68 ProgenyLate/Early 90Y20/94Y22 21 43 113 70 Progeny Late/Late 90Y20/94Y22 24 46115 69 Progeny Early/— 90Y20/94Y22 46 36 103 67 Progeny —/Early90Y20/94Y22 43 38 106 68 Progeny —/Late 90Y20/94Y22 48 42 110 68 ProgenyLate/— 90Y20/94Y22 45 45 114 69 Progeny Early/Early 90Y90 — 35  97 62Check Late/Late 93Y82 — 47 NA NA Check Early/Early 90Y90/93Y82 49 37 10063 Progeny Early/Late 90Y90/93Y82 44 39 104 65 Progeny Late/Early90Y90/93Y82 37 42 111 69 Progeny Late/Late 90Y90/93Y82 54 47 115 68Progeny Early/— 90Y90/93Y82 93 38 102 64 Progeny —/Early 90Y90/93Y82 8639 105 66 Progeny —/Late 90Y90/93Y82 98 43 110 67 Progeny Late/—90Y90/93Y82 91 45 113 68 Progeny Early/Early 91Y20 — 35  97 62 CheckLate/Late 93Y82 — 47 NA NA Check Early/Early 91Y20/93Y82 69 37 101 65Progeny Early/Late 91Y20/93Y82 63 39 107 68 Progeny Late/Early91Y20/93Y82 65 42 113 71 Progeny Late/Late 91Y20/93Y82 68 46 116 70Progeny Early/— 91Y20/93Y82 132 38 104 66 Progeny —/Early 91Y20/93Y82134 39 107 68 Progeny —/Late 91Y20/93Y82 131 43 112 69 Progeny Late/—91Y20/93Y82 133 44 114 70 Progeny Early/Early 91Y40 — 37 101 64 CheckEarly/Early 91Y62 — 36 101 65 Check Late/Early 91Y81 — 37 106 69 CheckEarly/Late 91Y92 — 34 109 75 Check Late/Early 92Y11 — 38 107 69 CheckLate/Early 92Y31 — 39 112 73 Check Late/Early 92Y53 — 39 110 71 CheckLate/Early 92Y60 — 41 115 74 Check Late/Early 92Y74 — 39 113 74 CheckLate/Early 92Y83 — 40 115 75 Check Late/Early 92Y91 — 39 114 75 CheckLate/Late 93Y22 — 45 NA NA Check Late/Late 93Y82 — 47 NA NA CheckLate/Late 94Y22 — 49 NA NA Check

Example 6

Several segregating populations in one or more locations were genotypedusing one or more markers, which in some cases included markersassociated with reproductive growth, as well as phenotyped for one ormore reproductive stages. Initiation of flowering was measured both asdays after planting (DAP), and as day of the year (DOY), which helpsaccount for different planting dates across locations where relevant.Marker data and phenotypic data associations were analyzed using apartial least squares (PLS) methodology. Tables 15-23 summarize thesestudies, Tables 20-23 show single location results which are alsoaggregated for analysis and presentation in Table 19.

TABLE 15 Allelic Pop (♀/♂) Locus Position SNP μFLDATE (DAP) Sub (n) Locs(ch) (cM) ♀ ♂ ♀ ♂ (DAP) 92Y75/92Y22 1 S09951-1 32.04 G_G T_T 41.7 39.62.0 (319) (11) S00170-1 45.37 A_A T_T 41.6 39.7 2.0 (11) S08519-1 8.96C_C G_G 41.2 40.4 0.8 (1) S08942-1 80.59 G_G C_C 40.3 41.5 1.2 (4)S02780-1 41.85 G_G A_A 40.6 40.4 0.2 (7) S02777-1 129.25 T_T C_C 40.040.9 0.9 (10) S04059-1 75.42 G_G A_A 40.5 41.4 0.9 (14) Variance (DAP orDOY) 11.0 Mean (DAP) 40.8 Mean (DOY) 181.8

TABLE 16 Allelic Pop (♀/♂) Locus Position SNP μFLDATE (DAP) Sub (n) Locs(ch) (cM) ♀ ♂ ♀ ♂ (DAP) 92Y75/92Y80 1 S08575-1 58.78 A_A G_G 65.1 66.31.1 (304) (2) S08942-1 80.59 G_G C_C 65.1 66.2 1.1 (4) S13139-1 97.08C_C T_T 64.9 66.3 1.4 (6) S06925-1 28.92 G_G A_A 66.5 65.1 1.3 (11)S13446-1 92.65 T_T C_C 65.4 66.3 0.9 (15) S01452-1 73.34 C_C T_T 66.264.9 1.2 (17) S01109-1 0.92 T_T G_G 66.2 64.9 1.3 (18) S10293-1 85.1 A_AG_G 66.7 64.7 2.0 (20) Variance (DAP or DOY) 8.2 Mean (DAP) 65.7 Mean(DOY) 176.7

TABLE 17 Allelic Pop (♀/♂) Locus Position SNP μFLDATE (DAP) Sub (n) Locs(ch) (cM) ♀ ♂ ♀ ♂ (DAP) 93Y30/92Y22 1 S01481-1 89.53 G_G T_T 50.3 45.94.4 (136) (19) Variance (DAP or DOY) 8.2 Mean (DAP) 47.4 Mean (DOY)189.4

TABLE 18 Allelic Pop (♀/♂) Locus Position SNP μFLDATE (DAP) Sub (n) Locs(ch) (cM) ♀ ♂ ♀ ♂ (DAP) 92Y60/92Y32 1 S01008-1 87.09 C_C G_G 42.9 41.81.1 (174) (7) S09955-1 58.82 C_C T_T 41.6 43.2 1.6 (12) S07851-1 83.76A_A G_G 43.6 42.2 1.4 (14) S11993-1 99.75 A_A G_G 42.1 42.1 0.1 (17)S13844-1 85.55 T_T G_G 43.6 41.7 1.8 (18) S08034-1 71.47 C_C G_G 41.842.8 1.0 (20) Variance (DAP or DOY) 10.3 Mean (DAP) 42.6 Mean (DOY)183.6

TABLE 19 Allelic Pop (♀/♂) Locus Position SNP μFLDATE (DAP; DOY) Sub (n)Locs (ch) (cM) ♀ ♂ ♀ ♂ (DAP; DOY) 91Y90/92Y22 4 S08942-1 80.59 G_G C_C46.1; 178.8 50.4; 177.7 4.3; 1.1 (1253) (4) S10631-1 94.2 T_T C_C 44.8;175.5 50.1; 180.4 5.3; 4.9 (10) S01574-1 99.5 C_C A_A 44.6; 174.7 50.1;180.5 5.5; 5.7 (10) S04660-1 106.5 T_T C_C 48.1; 180.1 48.1; 176.7 0.0;3.4 (18) S01481-1 89.53 G_G T_T 49.3; 180.8 46.9; 176.4 2.4; 4.4 (19)S11320-1 92.18 A_A T_T 49.5; 180.6 46.9; 176.7 2.6; 3.9 (19) Variance(DAP; DOY) 60.3; 51.1 Mean (DAP) 48.4 Mean (DOY) 178.1

TABLE 20 Allelic Pop (♀/♂) Locus Position SNP μFLDATE (DAP) Sub (n) Locs(ch) (cM) ♀ ♂ ♀ ♂ (DAP) 91Y90/92Y22 1 S08942-1 80.59 G_G C_C 41.0 41.90.8 (254) (4) S10631-1 94.2 T_T C_C 38.5 43.3 4.8 (10) S01574-1 99.5 C_CA_A 37.9 43.2 5.2 (10) S04660-1 106.5 T_T C_C 41.6 40.9 0.7 (18)S01481-1 89.53 G_G T_T 43.2 39.3 3.9 (19) S11320-1 92.18 A_A T_T 43.039.9 3.2 (19) Variance (DAP or DOY) 18.3 Mean (DAP) 41.2 Mean (DOY)182.2

TABLE 21 Allelic Pop (♀/♂) Locus Position SNP μFLDATE (DAP) Sub (n) Locs(ch) (cM) ♀ ♂ ♀ ♂ (DAP) 91Y90/92Y22 1 S08942-1 80.59 G_G C_C 44.3 48.13.8 (337) (4) S10631-1 94.2 T_T C_C 41.3 48.4 7.1 (10) S01574-1 99.5 C_CA_A 40.8 48.6 7.8 (10) S04660-1 106.5 T_T C_C 48.1 44.3 3.8 (18)S01481-1 89.53 G_G T_T 48.4 43.6 4.8 (19) S11320-1 92.18 A_A T_T 48.443.8 4.6 (19) Variance (DAP or DOY) 28.3 Mean (DAP) 46.1 Mean (DOY)178.1

TABLE 22 Allelic Pop (♀/♂) Locus Position SNP μFLDATE (DAP) Sub (n) Locs(ch) (cM) ♀ ♂ ♀ ♂ (DAP) 91Y90/92Y22 1 S08942-1 80.59 G_G C_C 59.6 58.21.4 (334) (4) S10631-1 94.2 T_T C_C 56.8 59.7 2.9 (10) S01574-1 99.5 C_CA_A 56.6 59.9 3.2 (10) S04660-1 106.5 T_T C_C 59.8 57.8 2.0 (18)S01481-1 89.53 G_G T_T 59.1 58.2 1.0 (19) S11320-1 92.18 A_A T_T 59.657.9 1.7 (19) Variance (DAP or DOY) 6.5 Mean (DAP) 58.5 Mean (DOY) 169.5

TABLE 23 Allelic Pop (♀/♂) Locus Position SNP μFLDATE (DAP) Sub (n) Locs(ch) (cM) ♀ ♂ ♀ ♂ (DAP) 91Y90/92Y22 1 S08942-1 80.59 G_G C_C 45.3 46.81.4 (328) (4) S10631-1 94.2 T_T C_C 42.4 48.6 6.2 (10) S01574-1 99.5 C_CA_A 41.8 48.6 6.8 (10) S04660-1 106.5 T_T C_C 46.1 45.6 0.4 (18)S01481-1 89.53 G_G T_T 48.1 44.3 3.7 (19) S11320-1 92.18 A_A T_T 47.944.6 3.3 (19) Variance (DAP or DOY) 24.0 Mean (DAP) 45.9 Mean (DOY)183.9

Example 7

From the analyses of marker loci associated with reproductive stage insoybean populations and varieties, several markers were developed,tested, and confirmed, as summarized in preceding tables. Anymethodology can be deployed to use this information, including but notlimited to any one or more of sequencing or marker methods.

In one example, sample tissue, including tissue from soybean leaves orseeds can be screened with the markers using a TAQMAN® PCR assay system(Life Technologies, Grand Island, N.Y., USA).

TAQMAN® Assay Conditions

Reaction Mixture (Total Volume=5 μl):

Genomic DNA (dried) 16 ng DDH20 2.42 μl Klearkall Mastermix 2.5 μlForward primer (100 μM) 0.0375 μl Reverse primer (100 μM) 0.0375 μlProbe 1 (100 μM) 0.005 μl Probe 2 (100 μM) 0.005 μlReaction Conditions:

94° C. 10 min 1 cycle 40 cycles of the following: 94° C. 30 sec 60° C.60 sec

Klearkall Mastermix is available from KBioscience Ltd. (Hoddesdon, UK).

A summary of the alleles for markers associated with reproductive growthphenotype in soybean is provided in Table 24. Marker S17691-001-Q001detects a deletion event, as reported in the tables “D” represents thedeletion.

TABLE 24 Genetic Allele Marker (cM) Physical (bp) polymorphismS01435-1-Q001 33.61 Gm05:30568085 A/T S01239-1-A 40.49 Gm08:7464336 A/GS00780-1-A 76.47 Gm08:15841570 A/G S06925-1-Q1 28.92 Gm11:4674824 C/TS09951-1-Q1 32.04 Gm11:5231500 G/T S00170-1-A 45.37 Gm11:7847341 A/TS04059-1-A 75.42 Gm14:46138053 A/G S07851-1-Q1 83.76 Gm14:47331319 A/GS11659-1-Q1 29.24 Gm04:5754268 C/T S04279-1-A 45.75 Gm04:8295779 A/TS02211-1-A 54.48 Gm04:39691731 A/G S08942-1-Q1 80.59 Gm04:44725098 C/GS05742-1-Q1 4.88 Gm06:410442 G/T S09155-1-Q1 69.29 Gm06:11659627 A/GS02037-1-A 89.19 Gm06:15457913 A/G S13136-1-Q1 94.84 Gm06:16391391 A/GS17291-001-K001 96.04 Gm06:16499786 C/T S13139-1-Q1 97.08 Gm06:16593381C/T S17292-001-K001 97.84 Gm06:16670047 A/G S13146-1-Q1 98.23Gm06:16804435 A/G S17293-001-K001 100.29 Gm06:17498270 A/GS17294-001-K001 101.72 Gm06:18203964 C/T S17581-001-Q008 102.13Gm06:19743496 G/A S17691-001-Q001 102.2 Gm06:19986645 D/IS17701-001-Q001 102.2 Gm06:20007173 G/C S03703-1-Q1 102.26 Gm06:20084642C/T S17297-001-K001 102.43 Gm06:20501491 A/T S17298-001-K001 102.71Gm06:21197184 A/C S17299-001-K001 102.83 Gm06:21500085 C/TS17300-001-K001 102.93 Gm06:22501610 C/T S17301-001-K001 102.97Gm06:22700011 A/G S17306-001-K001 103.29 Gm06:25700006 A/GS17310-001-K001 103.3 Gm06:28501458 G/T S17311-001-K001 103.3Gm06:28671736 C/T S17312-001-K001 103.3 Gm06:29499523 G/TS17313-001-K001 103.31 Gm06:30203054 C/G S17316-001-K001 103.31Gm06:31694650 A/G S17317-001-K001 103.31 Gm06:32503141 A/CS17318-001-K001 103.32 Gm06:33196184 C/T S17322-001-K001 103.37Gm06:35509548 C/G S17326-001-K001 103.79 Gm06:37712913 A/CS17327-001-K001 104 Gm06:38467854 C/T S17328-001-K001 104.25Gm06:39168136 C/T S17329-001-K001 104.38 Gm06:39533730 G/T S10746-1-Q1104.94 Gm06:40766974 A/G S17331-001-K001 105.8 Gm06:41476201 C/TS17332-001-K001 106.19 Gm06:42450296 A/T S17337-001-K001 113.1Gm06:47500976 C/T S13093-1-Q1 113.11 Gm06:47521797 C/T S12211-1-Q1116.04 Gm06:48475049 C/T S04555-1-Q1 132.43 Gm06:49978151 A/GS08519-1-Q1 8.96 Gm01:759365 C/G S12876-1-Q1 29.48 Gm02:4893148 C/GS05937-1-Q1 48.44 Gm02:9714426 A/C S08575-1-Q1 58.78 Gm02:11502780 A/GS08669-1-Q1 76.53 Gm02:15446229 C/T S11212-1-Q1 83.28 Gm02:33158449 G/TS00543-1-A 103.71 Gm02:45776142 G/T S01452-1-A 73.34 Gm17:16136646 C/TS11993-1-Q2 99.75 Gm17:39804515 C/T S13446-1-Q1 92.65 Gm15:50237460 C/TS00252-1-A 0 Gm13:235439 A/T S04060-1-A 36.9 Gm13:20365663 C/GS02664-1-A 36.96 Gm13:20744030 A/G S00281-1-A 73.16 Gm13:35174140 C/TS01109-1-Q002 0.92 Gm18:305113 A/C S13844-1-Q1 85.55 Gm18:58086324 G/TS05058-1-Q1 105.85 Gm18:61591142 A/G S04660-1-A 106.5 Gm18:61831970 C/TS09955-1-Q1 58.82 Gm12:11512115 C/T S08034-1-Q1 71.47 Gm20:39051858 C/GS10293-1-Q1 85.1 Gm20:41216234 A/G S03813-1-A 30.57 Gm16:4678569 A/GS02042-1-A 85.53 Gm16:36524407 A/G S16601-001-Q001 87.73 Gm19:47535046A/C S01481-1-A 89.53 Gm19:47826727 G/T S11309-1-Q1 91.1 Gm19:48252040A/T S11320-1-Q1 92.18 Gm19:48638646 A/T S04040-1-A 100.89 Gm19:50222676G/T S00863-1-A 8.09 Gm07:1141099 A/T S17151-001-K001 11.64 Gm07:1830296A/G S17153-001-K001 12.12 Gm07:1923026 A/C S17154-001-K001 13.97Gm07:2179883 C/T S17156-001-K001 15.53 Gm07:2310058 A/G S17159-001-K00118.14 Gm07:2679749 A/G S08590-1-Q1 19.96 Gm07:3009018 A/GS17242-001-K001 31.68 Gm07:4282676 A/C S17166-001-Q006 31.87Gm07:4319368 C/T S17167-001-Q007 31.99 Gm07:4342479 A/G S08539-1-Q136.74 Gm07:5576650 A/G S17178-001-K001 40.59 Gm07:6288899 C/TS17179-001-K001 40.83 Gm07:6340656 A/G S17180-001-K001 40.85Gm07:6347675 A/C S17181-001-K001 41.66 Gm07:6614649 C/G S17182-001-K00141.66 Gm07:6616695 A/T S17183-001-K001 41.69 Gm07:6623333 G/TS02780-1-Q1 41.85 Gm07:6671535 A/G S12107-1-Q1 43.16 Gm07:7096376 G/TS03624-1-Q001 45.02 Gm07:7774056 A/G S01953-1-A 48.13 Gm07:8674220 C/TS00111-1-A 79.14 Gm07:35590550 A/G S04180-1-A 86.05 Gm07:36459825 A/GS01008-1-B 87.09 Gm07:36638366 C/G S12862-1-Q1 53.56 Gm03:38491492 C/TS12867-1-Q002 58.35 Gm03:39583405 A/G S04966-1-Q1 92.16 Gm03:46209939A/T S10631-1-Q1 94.2 Gm10:43974548 C/T S01574-1-A 99.5 Gm10:44725777 A/CS16594-001-Q010 99.55 Gm10:44732850 A/T S02777-1-A 129.25 Gm10:50495033A/G

Table 25 summarizes exemplary allele polymorphisms and furtherassociates them with early or late phenotype for time to floweringand/or maturity. In some instances, the allele polymorphisms in Table 25represent the complement of calls provided in Table 24.

TABLE 25 Allele Genetic polymorphism Marker (cM) Physical (bp)(Early/Late) S17581-001-Q008 102.13 Gm06:19743496 T/C S17691-001-Q001102.2 Gm06:19986645 D/I S03703-1-Q1 102.26 Gm06:20084642 T/CS16601-001-Q001 87.73 Gm19:47535046 C/A S01481-1-A 89.53 Gm19:47826727T/G S17166-001-Q006 31.87 Gm07:4319368 T/C S17167-001-Q007 31.99Gm07:4342479 A/G S01574-1-A 99.5 Gm10:44725777 A/C S16594-001-Q010 99.55Gm10:44732850 A/TA summary of exemplary marker sequences is provided in Tables 26 and 27.

TABLE 26 SEQ SEQ Region Locus Primers (FW/REV) ID Probes ID SEQ ID NO:S01435-1 GCCTCTACTAGAA 1 6FAM-cagtacTttcgtcaataa 3 5 TCCGTGCATACGGAAGTGCTCTTG 2 VIC-cagtacAttcgtcaataa 4 GAACACAAT S01239-1tgagaattgatgctcatttagg 6 6FAM-acttgttaAcagcattc 8 10 aaccctagtacattttccctct 7 VIC-ttgttaGcagcattc 9 S00780-1 TGTAGTCCCATTG 116FAM- 13 15 CCATATGAGGC CTCGTTTTAAaCCTTCT CATTAGGGGTTTC 12 VIC- 14ACCACTGTCCA CTCGTTTTAAgCCTTC S06925-1 tgaggggaaattaagaaattg 166FAM-caccgTgatgctatt 18 20 g tgaggggaaattaagaaattg 17VIC-catcattttcaccgCgat 19 g S09951-1 tgccgtaagtaacacacacaa 216FAM-cacttgattAaattcctgt 23 25 a caagagcacaccatcacctg 22VIC-cttgattCaattcct 24 S00170-1 GCTGATACCGTTT 26 6FAM- 28 30 TGGTGTTTCCATGCATCTGCaGACGT TGCAACATCCCGT 27 VIC- 29 GAAAGGATT TGCATCTGCtGACGTGS04059-1 caccatcagcaagctttgag 31 6FAM-cctctgagttAgcctt 33 35gaagggcacttcaacagagc 32 VIC-ctctgagttGgcctt 34 S07851-1cttttccttggacggtacga 36 6FAM-CactgTacaaatcaa 38 40 cgtgtgaatggaagaaagca37 VIC-cactgCacaaatc 39 S11659-1 tctgtcccaatgctcaatca 416FAM-catgatgAcaacctc 43 45 cttggaggggaaggtctagc 42 VIC-atgatgGcaacctcta44 S04279-1 aacaactccctctggtgtcc 46 6FAM-atctccttcTcttcctt 48 50cataggggagtagattatatg 47 VIC-tctccttcActtcct 49 gcttt S02211-1cctctctcattctcgttcacgat 51 6FAM-caatttaTcgtaacatcag 53 55 gtaacttaggttcatttaaattccattt 52 VIC-caatttaCcgtaacatc 54 gct S08942-1cgtgatcctacgcctctctt 56 6FAM-tcacgatcgCagtct 58 60 aggtcatgtccacgacgaa57 VIC-tcacgatcgGagtct 59 S05742-1 acgacgtcaagaagttcctac 616FAM-tccgaaatcAtaatc 63 65 ggccgaactcggttctaatc 62 VIC-ccgaaatcCtaatcc64 S09155-1 ctattgccgagaagctcgat 66 6FAM-caacgtaTgtcatca 68 70tcatcctccgtgagatagcc 67 VIC-caacgtaCgtcatca 69 S02037-1tccatcaacaaagccca 71 6FAM-aatgcttcAagatca 73 75 aaaatatctagttgagttggac72 VIC-atgcttcGagatcaa 74 caaga S13136-1 cgtgcgccctatcagtctat 766FAM-accaccaTgtcgc 78 80 gagttgttgcttgcattgga 77 VIC-accaccaCgtcgc 79S17291-001 N/A — GAAGGTGACCAAGTTC 82 84 ATGCTTTTCCTTTTGCT ATTTTTGACTCGGAGGGCAATAGTTT 81 GAAGGTCGGAGTCAAC 83 GAAGATTTGGGAT GGATTAACTTTTCCTTT GAATGCTATTTTTGACTCGA S13139-1 aatctaccccgtacttgg 85 6FAM-agatcccAttcatg 8789 ttgcagaggcaaatagagctt 86 VIC-tatatagatcccGttcatg 88 S17292-001 N/A —GAAGGTGACCAAGTTC 91 93 ATGCTCAATGTAATCA TTTAAGTACATTATCCC ACACRGGACACATTTT 90 GAAGGTCGGAGTCAAC 92 TAGCTTACGTAGT GGATTAATGTAATCAT TAAATTAAGTACATTATCCC ACG S13146-1 gtcatcatagccgcaatcaa 946FAM-aagttcatcAaagccat 96 98 tccaaatctttgttgagtcgtg 95VIC-aagttcatcGaagcca 97 S17293-001 N/A — GAAGGTGACCAAGTTC 100 102ATGCTGTGTTTTAACTC ACTCAGTTTCGAATGT GCCTAAAGACCA 99 GAAGGTCGGAGTCAAC 101ACAATTTGTAAGA GGATTGTTTTAACTCA GTAAA CTCAGTTTCGAATGC S17294-001 N/A —GAAGGTGACCAAGTTC 104 106 ATGCTAGAAAGTAAGG AAAATTTCTAATTTTCA TTGCCACACAGGAGAC 103 GAAGGTCGGAGTCAAC 105 AAATCAYGTCGAT GGATTGAGAAAGTAAG AAGAAAATTTCTAATTTTC ATTGT S17581-001 ACGAATGCAAAA 1076FAM-ttgaggacgtgtagTtg 109 111 TTGGAAATG TCTTCCTTCGTCC 108VIC-ttgaggacgtgtagCtgt 110 GTGTCA S17691-001 CCTCTTTTCCTTG 112VIC-cttctcatcattgtggac 114 115 GCTATGTGAT CAATCTTAACATG 113 N/A —GTTCCAAAACA S17701-001 GACCCTATTCATC 116 6FAM-tggatacCtcttctt 118 120TCTTCCAACA GATGTCCTAAAGT 117 VIC-atggtggatttcGtc 119 TAGAGGCTTCGS03703-1 cccaaggactaaccaggatt 121 6FAM-acacaagTcgctacc 123 125 Ctttattaaatggagtgagaagg 122 VIC-cacaagCcgctacc 124 tgtc S17297-001 N/A -GAAGGTGACCAAGTTC 127 129 ATGCTCACAACACTAT TTAATTTATTTCTGAAA AGCAAGTAAGAAAGTTTT 126 GAAGGTCGGAGTCAAC 128 TTTGTGTGTAAAC GGATTCACAACACTATTGAT TTAATTTATTTCTGAAA AGCAT S17298-001 N/A - GAAGGTGACCAAGTTC 131 133ATGCTCTCGCTTAGAG GAAGAACGTGTA CTCGCGCTTGAAG 130 GAAGGTCGGAGTCAAC 132GCATCAATCTT GGATTCTCGCTTAGAG GAAGAACGTGTC S17299-001 N/A -GAAGGTGACCAAGTTC 135 137 ATGCTGACTACCACCA CGCGTCATAG GGCCTTTTACATC 134GAAGGTCGGAGTCAAC 136 GGTTCTAATGACT GGATTGGACTACCACC TTT ACGCGTCATAAS17300-001 N/A - GAAGGTGACCAAGTTC 139 141 ATGCTCATATAAGTAGAGATGTCAAATTTTCG AC TTGTGAAGGACAC 138 GAAGGTCGGAGTCAAC 140 TCAACTATTCCACGGATTAATCATATAAG TA TAGAGATGTCAAATTT TCGAT S17301-001 N/A -GAAGGTGACCAAGTTC 143 145 ATGCTATACTTTATCCT GAGTATTTCTCATGAT CTCCCTATCACCTGT 142 GAAGGTCGGAGTCAAC 144 CATATACCCCTT GGATTCTTTATCCTGAGTATTTCTCATGATCC GAAGGTGACCAAGTTC S17306-001 N/A - ATGCTATTTTTAAGAA 147149 ACATGTTTTTAGGAAA CTATA CCCTCATCCTTCT 146 GAAGGTCGGAGTCAAC 148CCATGGGATTTT GGATTATTTTTAAGAA ACATGTTTTTAGGAAA CTATG S17310-001 N/A -GAAGGTGACCAAGTTC 151 153 ATGCTGAAAATACGCA AGGAGCTCTGTTC TCATTGATGGTGC150 GAAGGTCGGAGTCAAC 152 CTCTTTATTGCAC GGATTCGAAAATACGC TTTAAGGAGCTCTGTTA S17311-001 N/A - GAAGGTGACCAAGTTC 155 157ATGCTAAGTATCCTAT TACAACCATCAACGG CGCAGGAGTCATG 154 GAAGGTCGGAGTCAAC 156GATCTTGTCAAT GGATTGATAAGTATCC TATTACAACCATCAAC GA S17312-001 N/A -GAAGGTGACCAAGTTC 159 161 ATGCTAAGAAAGAAAA TCACGCAACATAAATG TTGGAAGACCAACGC 158 GAAGGTCGGAGTCAAC 160 GTTCTCTACTTGT GGATTAAAAAGAAAG TAAAATCACGCAACATA AATGTTT S17313-001 N/A - GAAGGTGACCAAGTTC 163 165ATGCTGGTACGGCCTC GATCACACC AGTCCTTTGAAGA 162 GAAGGTCGGAGTCAAC 164GGAGGACGTGTA GGATTGGTACGGCCTC GATCACACG S17316-001 N/A -GAAGGTGACCAAGTTC 167 169 ATGCTAAGAGCTTCCA TTTTCGATTACGAA TCGGATGTTCGAT166 GAAGGTCGGAGTCAAC 168 TGTGTCCCATAAT GGATTAAGAGCTTCCA ATATTTTCGATTACGAG S17317-001 N/A - GAAGGTGACCAAGTTC 171 173ATGCTTGAGAAAATCC CTCCTCCATTTTA GAGTTGGTGAACT 170 GAAGGTCGGAGTCAAC 172AATTTTCCCTGTT GGATTCTTGAGAAAAT GAT CCCTCCTCCATTTTC S17318-001 N/A -GAAGGTGACCAAGTTC 175 177 ATGCTAACAGGAAGGG AAAACAAAGTGTCG CCTTGATGCTCTA174 GAAGGTCGGAGTCAAC 176 TTTCTTTTCTCCCA GGATTGAACAGGAAGG AGAAAACAAAGTGTCA GAAGGTGACCAAGTTC S17322-001 N/A - ATGCTATTTTGGGTTTT 179181 TTTTTGTAAAAACAGA AAGTC ATGTTGTTTGTGT 178 GAAGGTCGGAGTCAAC 180AGATTAACATCGG GGATTTTGGGTTTTTTT CTTT TTGTAAAAACAGAAAG TG S17326-001N/A - GAAGGTGACCAAGTTC 183 185 ATGCTAAAATAGCTGA AATTGCATTTATGGTG CAACACAACACTGCTT 182 GAAGGTCGGAGTCAAC 184 ACAGCAAATTGCA GGATTATAGCTGAAATTAA TGCATTTATGGTGCAC S17327-001 N/A - GAAGGTGACCAAGTTC 187 189ATGCTAAGTAGCAGTT AAAGAGGACTGGTC GACCTCATATGAA 186 GAAGGTCGGAGTCAAC 188AGAATATGTCCAA GGATTAAAAGTAGCAG TCTT TTAAAGAGGACTGGTT S17328-001 N/A -GAAGGTGACCAAGTTC 191 193 ATGCTATCCACCTTGCT TTACAATGCATCC TTCTACAAGGCGA190 GAAGGTCGGAGTCAAC 192 AGGACCATTTTAT GGATTCATCCACCTTG CATCTTTACAATGCATCT S17329-001 N/A - GAAGGTGACCAAGTTC 195 197ATGCTCCTTTGCTTCTT GAAGATCATGGC CTCCAATCATCTT 194 GAAGGTCGGAGTCAAC 196TCTTCCTTCTCCAT GGATTGTCCTTTGCTTC TT TTGAAGATCATGGA S10746-1attgggatcctgatcaacca 198 6FAM-caacaaTgagcctaat 200 202cccaggcattggtgtttaag 199 VIC-caacaaCgagcctaa 201 S17331-001 N/A -GAAGGTGACCAAGTTC 204 206 ATGCTGGGAAATGAAG ACAATTAATAACATCG TGCGGTTGTCTCTGS 203 GAAGGTCGGAGTCAAC 205 TCTTCTCAGATT GGATTGGGAAATGAAGACAATTAATAACATCG TA S17332-001 N/A - GAAGGTGACCAAGTTC 208 210ATGCTCAAACCTTAGG ATAGATGACTTCTTGTT AACCTTACCCTAA 207 GAAGGTCGGAGTCAAC209 CAACATACAACTA GGATTCAAACCTTAGG AGAA ATAGATGACTTCTTGT A S17337-001N/A - GAAGGTGACCAAGTTC 212 214 ATGCTTGATTGATAAT TTTTTTTATTATGTACA TGACCCTATTGACCGTG 211 GAAGGTCGGAGTCAAC 213 ATATTAATTAAGA GGATTGATTGATAATTCTTT TTTTTTATTATGTACAT GAT S13093-1 catcgagtctccagcaagtg 2156FAM-attggcacttTtaac 217 219 tgagattcacgaagtgggttc 216VIC-cacttCtaacatcaatg 218 S12211-1 gaccagaggtagtagattcca 2206FAM-ctgcaaTgccatact 222 224 aaagt tgcattaagctcactcagttat 221VIC-ctgcaaCgccatac 223 gtatta S04555-1 AAATCGCCACTAG 2256FAM-cagcacTggatctt 227 229 GCTTGC CTAGGGTTCTGCA 226 VIC-cagcacCggatct228 GTTCATCG S08519-1 acagttcattggccttgaca 230 6FAM-tcagctctgCcaatag 232234 ggcttcacacttgaggaggt 231 VIC-tcagctctgGcaatag 233 S12876-1cccgccacaactcttgttat 235 6FAM-cacgcttcCaatct 237 239gggaggtgtttggcaatatc 236 VIC-aagcacgcttcGaat 238 S05937-1gcaaaattaaggagaggacc 240 6FAM-catcAgctatgaccatg 242 244 ttgctctcttgcaaaatgcacca 241 VIC-catcCgctatgacc 243 S08575-1aactatgcacttatgctcatgg 245 6FAM-acttcttgcTgaatct 247 249 taatggatccaaacatgcgtcta 246 VIC-aacttcttgcCgaatc 248 S08669-1gtggtgggttggtttttgac 250 6FAM-tcttatgggacatTtc 252 254tccaatattctcagcctcttcag 251 VIC-tcttatgggacatCtc 253 S11212-1ctccaagaccttgccttcct 255 6FAM-ccccgTttacttcc 257 259gatcccaaatgagattaggag 256 VIC-cccgGttacttcc 258 act S00543-1GCATGCAATATGA 260 6FAM- 262 264 ACAACTTGACAAC CACTTATCCAtTGGTTCCCCTTTTCACATG 261 VIC- 263 AGTATGCATGTC CACTTATCCAgTGGTTC S01452-1caaacaatgaatgatgaatcc 265 6FAM-aagcaaTtgg-tcacaac 267 269 aagcattttgagagccaccaata 266 VIC-aagcaaCtggtcacaa 268 S11993-1atttgtgagtgctgcggatt 270 6FAM-ccagcacaatTgat 272 274tgaacatgaacgtgctaaacg 271 VIC-ccagcacaatCga 273 S13446-1atcccaggcttctaatgtgg 275 6FAM-cccaccacActca 277 279 ggctgcgctactttcgtact276 VIC-cccaccacGctc 278 S00252-1 ATGCATGCAGCTG 280 6FAM- 282 284GGCAATAAT CGGTCTCtTGGTACTAT GATGCCACCGATG 281 VIC- 283 AAGAAGCACCGGTCTCaTGGTACTAT S04060-1 ctcttgcagcggattcagtc 285 6FAM-cgacttcaCtcacc287 289 ctcgccgatttcctcatct 286 VIC-acttcaGtcaccgagat 288 S02664-1GTTTTGGTTTCCTT 290 6FAM- 292 294 AGGATGAACT CTTTCCATCTTaTTCGATGTGCAGAGGTC 291 VIC- 293 CCATTCT CTTTCCATCTTgTTCG S00281-1GGCCGAGCAAAC 295 6FAM- 297 299 AACAAGAAAA CATAGTGaACCTCTC TCCAAACTCCTCA296 VIC- 298 CAAGCCTTCA CCATAGTGgACCTCT S01109-1 AGTAGTACTTCAT 3006FAM-ccaccaccTctgaaa 302 304 CCCTGACACCA AGGAGTATAACCT 301VIC-accaccGctgaaaa 303 TGGTTTAAAGCTG S13844-1 tgatggaaagccgaaaaaga 3056FAM-tcccttaAgtagtcta 307 309 ctgagcagccctcatatgta 306VIC-atcccttaCgtagtctt 308 S05058-1 aaatgatacgcaattttgactc 3106FAM-atagcAgttcattgtac 312 314 ag tgtgttatgcctaccaatcaaa 311VIC-atagcGgttcattgta 313 ct S04660-1 tcggccttcgtcatagaagt 3156FAM-catctacAtccttcc 317 319 tccttcaatttccccatatcc 316VIC-catctacGtccttcc 318 S09955-1 gatcgggatgaggaa 3206FAM-cacacttgaTactcca 322 324 cttttcatgatccaaccagaca 321VIC-cacacttgaCactcca 323 S08034-1 tcctactaaaccctgctgtg 3256FAM-caatccaCaggagcat 327 329 ttggtctctacttagtacatctc 326VIC-caatccaGaggagcat 328 a S10293-1 gggcatccagactttatctatg 3306FAM-tacTacagtcgatctc 332 334 a acgatttaatgcacgacgagt 331VIC-ttcCacagtcgatc 333 S03813-1 atttagcgtacatgtcaactaa 3356FAM-cctaacTagaatac 337 339 cga tgcaaatgctttgaatctgg 336VIC-cctaacCagaata 338 S02042-1 gccatatccatactgcaacc 3406FAM-ctccttgaggTtac 342 344 agaagcgttggctatgcacg 341 VIC-ctccttgaggCta343 ag S16601-001 TTCACACATGTAC 345 6FAM-cagcttcaAaacatt 347 349TAGGCTTTGG CCACCTTTCACAC 346 VIC-cagcttcaCaacatt 348 AGCTTGA S01481-1tacaggctggctgtactt 350 6FAM-cagtcacTttatggtcc 352 354actctgggtgccaaagtcaa 351 VIC-cagtcacGttatggtc 353 S11309-1gaccggtctgggacaatg 355 6FAM-atttcAtggttctcg 357 359cacttaatcaagttgcccaag 356 VIC-caatttcTtggttctc 358 aa S11320-1gcccaaagttcaaaagcaat 360 6FAM-aaacaAacgatctcaac 362 364tcggatgcgaatatgaagtg 361 VIC-aaacaTacgatctcaac 363 S04040-1cccagctgctgaggagaa 365 6FAM-aaggtacccTctagtg 367 369ggattgaaaaacaattggag 366 VIC-aaggtttcccGctagt 368 ga S00863-1CAGCATCACACAC 370 6FAM- 372 374 GCTATAAGACCA TCAACACTCACAaGATCATGACTTTTTCA 371 VIC- 373 TACTAAGTTGGAC TCAACACTCACAtGAT ACCAS17151-001 N/A - GAAGGTGACCAAGTTC 376 378 ATGCTGGAAAAAGAAGAAAAAATTCCACTAAT GTGA CRAGTCTCAGTCA 375 GAAGGTCGGAGTCAAC 377ATCTGTGACTCTT GGATTGAAAAAGAAG T AAAAAATTCCACTAAT GTGG S17153-001 N/A -GAAGGTGACCAAGTTC 380 382 ATGCTGCCCTTAATTG CTCAAATTTCCACTA CTGACGTGGAGTG379 GAAGGTCGGAGTCAAC 381 TGACAATGCAAT GGATTGCCCTTAATTG CTCAAATTTCCACTCS17154-001 N/A - GAAGGTGACCAAGTTC 384 386 ATGCTAAATGTTTTTCTCGTGCTTGATTGC GAACCACATTTCT 383 GAAGGTCGGAGTCAAC 385 AAGTTAAAGCGAGGATTMTAAATGTTTT CTTAA TCTCGTGCTTGATTGT S17156-001 N/A -GAAGGTGACCAAGTTC 388 390 ATGCTCAACAACTAAT TGACCCTGCAGG CCCTTCCAATGAA 387GAAGGTCGGAGTCAAC 389 ATAAAGCACTTGG GGATTAACAACTAATT AT GACCCTGCAGGS17159-001 N/A - GAAGGTGACCAAGTTC 392 394 ATGCTGGAAGACACGT GGTCCACCTTYCAGCCCAACAA 391 GAAGGTCGGAGTCAAC 393 ATCTCAAATGGGA GGATTGGAAGACACGT TGGTCCACCC S08590-1 cccttgaaagacgaccaaaa 395 6FAM-cagatcAgttgtcattt 397399 acttatccgcagccgtacac 396 VIC-cagatcGgttgtcatt 398 S17242-001 N/A -GAAGGTGACCAAGTTC 401 403 ATGCTTGGGGAATAAA CATCGTGCTTTATAATT ACAGAGTGCCTTGA 400 GAAGGTCGGAGTCAAC 402 CGTAGTGACATA GGATTGGGGAATAAACATCGTGCTTTATAATTC S17166-001 CCGCAAACTGTAG 404 6FAM-caagacaTgcagcaga 406408 TACAAATCAA GGGTTGTAGAAA 405 VIC-caagacaCgcagcag 407 GTAACTTGGGAAGS17167-001 GTTTTCACATGTA 409 6FAM-taactgtgcttttttaaaa 411 413ATTTTCAAAACAA A TGTCAGTGATGGT 410 VIC-taactgtgctCttttaa 412 GAAAATGATAGS08539-1 cacttctgtaaagagtcaaca 414 6FAM-agagattgaagaAtt 416 418 agaggtgaatacaccttgagtccaaa 415 VIC-tagagattgaagaGttt 417 gaa S17178-001 N/A -GAAGGTGACCAAGTTC 420 422 ATGCTACCACCATTCG GCTAAAGTCAATC GAATTGATATTTC419 GAAGGTCGGAGTCAAC 421 AACCATGGATGCA GGATTCACCACCATTC TCATGGCTAAAGTCAATT S17179-001 N/A - GAAGGTGACCAAGTTC 424 426ATGCTAAAAATATTTT CTAACTCTAAAAGCAA ACTGGA CCAGTTTACTTAG 423GAAGGTCGGAGTCAAC 425 TTAGGTGCCCAAA GGATTAATATTTTCTA TTA ACTCTAAAAGCAAACTGGG S17180-001 N/A - GAAGGTGACCAAGTTC 428 430 ATGCTGAAATGATAAAACCTAGTAAGCTTTCA GTT CAGTGCATTTCCC 427 GAAGGTCGGAGTCAAC 429ATAGAAAGTTATT GGATTAAATGATAAAA TGTT CCTAGTAAGCTTTCAG TG S17181-001 N/A -GAAGGTGACCAAGTTC 432 434 ATGCTGTAATCACTAA AATTACACACTTAAAT TACGGGCCAATTTTGT 431 GAAGGTCGGAGTCAAC 433 ATTACATCTTTCC GGATTGTAATCACTAAAGAA AATTACACACTTAAAT TAG S17182-001 N/A - GAAGGTGACCAAGTTC 436 438ATGCTGTAATAGGTCA TAAATGTTGATGGAAT ATTCT CTCAGATATACAT 435GAAGGTCGGAGTCAAC 437 AGATGAGAGGTG GGATTGTAATAGGTCA ACAA TAAATGTTGATGGAATATTCA S17183-001 N/A - GAAGGTGACCAAGTTC 440 442 ATGCTGATCGTGCGGTGGATGTGAAG ATRCGTGGCCACC 439 GAAGGTCGGAGTCAAC 441 ATTTACCTGTATTGGATTTGATCGTGCGG A TGGATGTGAAT S02780-1 attttccagactattgcctttac 4436FAM-actctggAtaacctg 445 447 ctt agaatacttgactgtataggat 444VIC-actctggGtaacctg 446 gcaaac S12107-1 cctcctcctcaaactgttgc 4486FAM-caatcggctccAtc 450 452 gtggcaaagtgcgaacaata 449 VIC-caatcggctccCtc451 S03624-1 TAGAATAATCACT 453 6FAM-agcatcattagtgTcacat 455 457ACAATAACAGAT GATCTTG CATTACATGCATA 454 VIC-agcatcattagtgCcacat 456ACCTCTCATCA S01953-1 GGAGTGTACTTCT 458 6FAM-ttccttctTcacttgat 460 462TTATGAAAAACGG TGA GTGTCGGGCCACT 459 VIC-tccttctCcacttgat 461AATTTTGGAGCCT TT S00111-1 ACTGATTCAAGAT 463 6FAM- 465 467 ACGATCAAGTTTCCCTAATTgCGTTTACC CTTATCATTT TTGGTTTTGGTGA 464 VIC- 466 ATAACTGGAAAACCTAATTaCGTTTACCC GTGTGT S04180-1 cattcaccatttatgaattttgat 4686FAM-cattgacActgttcct 470 472 cc aaatgaaaacccagaataatg 469VIC-cattgacGctgttcc 471 tgc S01008-1 atcccttgctttaactagattgtt 4736FAM-caattCctctgtaagtc 475 477 attcatgt atgcactggattgtgaagaga 474VIC-caattGctctgtaagtc 476 atataagc S12862-1 ggttcgagggttgtgtatcc 4786FAM-catttatcAgattcgatc 480 482 gattgcacccatatcgacct 479VIC-acatttatcGgattcga 481 S12867-1 CACACGTTAAAAC 4836FAM-accacatgtaactAtt 485 487 TCTTGTTCAGC TCCTAGAATAAAT ATGATCCCTTCTC484 VIC-accacatgtaactGtt 486 AT S04966-1 atacccagcagcagtcacca 4886FAM-catttgggtatgcTgtg 490 492 ttgtgtggccttacctttca 489VIC-catttgggtatgcAgtg 491 S10631-1 tttgatgcaagatctgtcgaa 4936FAM-ccaactcAgatctt 495 497 agccggtttacttggaatgtt 494 VIC-ccaactcGgatctt496 S01574-1 tgaagcaactaggaaagctg 498 6FAM-aaggcatcTttatctc 500 502 aaacgacccaatttgcttgtct 499 VIC-aaggcatcGttatct 501 S16594-001CACTACAGCCTCC 503 6FAM-catgtcttatgTaaatat 505 507 CGTGCT CCTCTGAAGAATA504 VIC-catgtcttatgAaaata 506 GCTTCCACTG S02777-1 acatatcgaagtgcaaatacg508 6FAM-ttgttatcttccActttag 510 512 g tcgacttgaaatggaaactga 509VIC-ttgttatcttccGcttta 511 a

TABLE 27provides the genomic region comprising the polymorphism associated with areproductive growth phenotype in soybean. Locus Genomic region SEQ IDS01435-1 TGTTGATGAGGGGGCCATATACCATCAGGAACATGCCAATGC 5TTATTAGAGAATGGAAACYTGATTTTAACCTGAAGCAAGACATGCTACGGACTCTTCCTATTTGGGTACAACTCCCTCAACTGCCATTGCATTTATGGGGTGGAAAAAGCCTAGGCAAAATTGGAAGTGCTCTTGGAACACAATTGGTTATTGACGAA[A/T]GTACTGCAAATAAACTTCGGGTCTCGTATGCACDGATTCTAGTAGAGGCAGATGTCACGCCAGAACTGAGAAACGAAATTACTATAAAGGACAATGAGGGGCGGAGGATCACTCAAAAAKTCGAATATGAGTGGAAACCAATGTTTTGTGATAAGTGCCAAAAGTTTGGCCAYAA ATGTGGTGAAGTAAAGCCAAGGAAGS01239-1 ATTTTTATAGTTATATTTCTCAAAATTATATTCAAGAATCAGA 10AAACAGAAAAATAATGTTATAAATTTSATGCATATCTTCCATTAAAACAGGTTAGATCCATAGTTGTTGCTAGTCAATAACCTTATGGTTAGCAGTGCCATCCCTTDCAACAATGAGAATTGATGCTCATTTAGGAAGTCAACACTTGTACTTGTTA[A/G]CAGCATTCYGGAAAGAAACAAGAGGGAAAATGAAACAAAGGGTGTTTTTCAAAAAATATTGGCTGATCATGATTTTTTGATCATGATTTTTACRTGTTCTGTTAAGACTAAAGTACATTAATTTCACTGTGTTGGCACCTGAATAGTTATTGAGCATTATGTGAGGTGGCAATTAAGTA TACAGTTTTGTCAYGACTTTTS00780-1 ACAATGAAGAAGGAAGTACTTTGCAGGTATTGCAATAAGAAG 15TTCAGTTGTTACCAAGCCTTGGGTGGACATCATAATTCTCACAAGGCGGAAAGAGCAGCAGAAATACATAGCAAGGCTTCTGCTTGTTACAAAACATATGGTTATGGGTTTTGTGGCAAAACATTAGGGGTTTCACCACTGTCCATGACTCGTTTTAA[A/G]CCTTCTATTATTGTTGGCCTCATATGGCAATGGGACTACATGACTGACTATCATCATGTTGCATGGCCAAGGCACCAGATTTTGAATCCTCCTCAACCCACCATGTATCAATTCATGGCTGAAGGGAGTGGATCTCACCAACACCACAAATTATATTARCCTTTGAGTTCTTCTATAGTC AGAGGAGGACCAACAAATTCS06925-1 AGTCCATTGAACATTCCTCATATTGTTCCATGCACTTTGTGTG 20AAACTGCAGTGGCACCGGTTCTTTTGGGGGAAGTAGATCAGCTTCAAAGATTGCAGCTTTTCATTTTGCTTATTTTCCATATTTTATGAGGGGAAATTAAGAAATTGGTTGTTAAATAGAGAAACAAAGATTTGTCTCCACTGCATCATTTTCACCG[C/T]GATGCTATTGCTATATCTTGTTCCATATTAGCTGTGAATCCTTGTCACTTATGGGGGATATTAGGCTTACCCGGGTAGAGCAAGGTCAAACAAAGATTAGAAATGTTCCAATTGCTGTCACCCCTGAAGGATTTTGGTGTTGCCMTACTCCTGTTGGGTTTCAGAAAAGCCTCAAACCTC AAAACCCTTTGAATAAACTCS09951-1 CGAGCCCTTGCTATAAAAACGGGACTGAAGCTCATTTCAACG 25GGGAAAATTCCCAAATCTGTTTTAGCTCGCCCCAACTGGCCATACACGTTGCTCCCACAGCTCAAGAGCACACCATCACCTGATATAGCATATAGTAAAAAACTTAAGTTTTGAAAACGCATGCATACATCTTAATGATCTAACTTGCTACAGGAATT[G/T]AATCAAGTGTTTGGTGTTTGTGTGTGTTACTTACGGCAAAGAATCAGAGAGTGATCAAGGCCACACGCAATGTCCAGAACATGAACACCGTGTAATTCTTCGACCAAGCGGGGYTCCCATACTATTGGCATGTTATTCTCCTGYTCCATTCCTTGCAAGACTCTCTTTTCAGCAGCTTC AWGGTCCKCGAGAGCTGTGAGS00170-1 TSACGAGTAGAATTTCNANTAGAATTTCAAGTAATTTTCGGAC 30TGAATCAAATAATCCAAACCAAAGAGTAGATTACAAGCCAGGTAAATTTTCAAGGATCCAAATGTGGTAGGACCAGGTCACTGGGATACACAATGCATCATATATATATGTACGTGCAACATCCCGTGAAAGGATTTTGCCTAGGTCGTTGCMCGTC[A/T]GCAGATGCATTTTATTTGTACCTAAGAATAATACACTCGAGTACACAGCTATTTATTTCAGTCTTGAGCACTTGAAAACATCATGTTAAGTCCACATAAATTCATTAAAGACATTGGAAACACCAAAACGGTATCAGCAACTGAGGCTATCCAAAGCCAGAGATCCAAAATTACAAAG GCAAAATGATAAAATACGGAATS04059-1 AAATTCCAAACGATTATTATTCTGGGAAGAGTCGAAGCACAA 35TACTCATTAACAAGAAAATTCGGTTGTACCCATAAAATACCGATTCCTACCCGCACTTAGATTGATCAGTACTTGTAGTCCTCAACATGGAGGCTCTCTGAGGCACCATCAGCAAGCTTTGAGTTACCCTTGTAGGTTCCCAGAGTTGCCTCTGAGTT[A/G]GCCTTGGCTCTTACCAAAAGGGCTTCCTGAGCCTTCTTCACATTCTCCTCTTTTCCACTCCATGCCTTAAGGGTGCTCTGTTGAAGTGCCCTTCCAAAGGAGAAAGAGAGTGACCATGGCTTCTTTCCATTGACCTGGTTAATGGCATTGAGGTTAACGGATGCCTCCTCCTCACTCTGC CCACCAGACAAGAAAACGATS07851-1 TGTAAAAGGTTTACGTAACCATACTGCAATTTRCAACCACAT 40GCTGCAGTCGTATCAGCTATATTTTCTTGTAACTGWGATTAATTATAATCGCAATCTAAATTCATTATTAGAGATAAATGACCACCATGCATCCTGATTTATGCGTGTGAATGGAAGAAAGCATATACAGATGTTGACATATCCAAGCATTGATTTGT[A/G]CAGTGATCTCCAAATATTTCGTACCGTCCAAGGAAAAGATCAGGCTCTAGCCACATATCTTCCGAGCCACATACATGAACTGAGCTTGAATCATATACCATAATTAGCATAAAAGGGATGAATTAATGCAGAGGAGTTTAATTATAAAGCTTTATTTTTCGCTTCARAGTTTCAGCA AGATTTTATATATATATATATATS11659-1 TAAAAATGATTTAATTATTATTAATTTAACTRTAGTTGAATGA 45TTGAATCTTGAACTAATACCTTCTTCTTCATTGATTGAATGGAAAATCTAATTTTATAAACATTGATTWGCCTCATTTGTCGAGGSCCACTAATGAAATGTGAGATTTCCTTGGAGGGGAAGGTCTWGCTCTAAAAAGCCCAGCTAGCTAGAGGTTG[C/T]CATCATGTACGCAATCTTAAATGATTGAGCATTGGGACAGAGCTTGCCATGTACTTTACTACCAATGCTCATATTTCCCMTGTTGATTGTGTCTCCCTTTCTATCTTTATATCAACTTTCCAAGTTGTTGACCATGTCCATGTACAAAGGATCATAGCTGCTCTTTTCTTTTTTCTTTCTGTT GTGCTTCTCACCTTACC S04279-1TAGATTAACTGCAAGGAGACACATTTCATCTTGAATTTTCTAT 50GTAACTTTGTATTACAACAAAGCCTTGTCCCGCTAGGTGAGGTCAGTTATATGGATCACACGATGCCATTTGACTTGGTTGAAGGCCAAATCTTAWGAGATATTATTTACCATGAGATCCCTCTTAACAACTCCCTCTGGTGTCCTTGATCTCCTTC[A/T]CTTCCTTTTCACAAAACTAAAAGCCATATAATCTACTCCCCTATGTAGCAGTGTAATACATCCTGGATTTTCTGTGAAAAGTTATACATTTTTTCAGAAAATTGAAGGTCCTATTTATTTTCATAATGGCCACATGTCTATATGATACACYCTTAGCCCATGTATATATAAAAAATATGGG CTGGGAAAGAAATGGCACA S02211-1GAGCTCTGCAAACAGATCTAGGAGGAGAGAGAGCGCACYGA 55GTTTCGTCTTCTTCAGGAGAAAGCTAGCCTCGTTTCGTAATTTCCCCTTTCCNATTCAATTTTATTTTTTTAGGGTTTTCAATTTGTACTGTAGTGTAAGTGAATTTGGAAAGATGCTTTTGGTTCATTTAAATTCCATTTGCTCGAACTGATGTTACG[A/G]TAAATTGCTTTTCTTTTTTACATCGTGAACGAGAATGAGAGAGGAATGGYGTGGCGACGTTGGCGTCACAGAGAAGGAAGAAGAAGAAGTGACGTTGATGAAGAAGAAGAGTAAGAGAAATGAGAGGGTTGGTGCCGCAAAGAAGGAATATGAAGAAGAATAAGAGAACGAAGAGG GAGCGGTGGTGCTCCACTGTGCATS08942-1 TTAAATAATTTTGTTAGATCTCTCTTATTTTTAAATATTTTATT 60TAAATATTTATTAAATTAATATAATTATGTAAATATTCGGTTTCTCTCCTTGTTTTTTTTTCTTCTATTTTTTATTTTTTTTTACTTCCCTCTCCCGTGATCCTACGCCTCTCTTCTTTCTTTTTCCTCCTTTTTTCTTTCCCTCCATCACGATCG[C/G]AGTCTCCTTTCACCTTCCCCTTCGTCGTGGACATGACCTCCCTCCCCCTTCCTTTCCGTCACGGCCTCCTCCCCATTCTCCTCCGTCGCGAGCCCCCTTTACTCCTTCCGAAACTCTATCACGACCTCCTTCCCCATGTGTCAATATGTATATTTTGTTTTTATGGTTTGTTTTTATTTGTTTCTTTTTAAT CATTCCAT S05742-1GAGAGGACTCCCAGGTTTGGGCTGGGACGATTTTCTGGGCTT 65CCAAACGCAGATAACTCTCTTTGGCAACAACTCCGCCACGGTCTTCCCGAAAACGGCGTCGTCCTGATGGATCAGATGCTCCCCCAGCTGTTCCTCCAGGTACTTGTCGAATTCGGGAGGGTCCTCGTGGCCGAACTCGGTTCTAATCTCCAGGATTA[G/T]GATTTCGGACTGCGTGTCGGAAAGGAACTTCTTGACGTCGTTGAGGACGAGGTCAACGCCGTAGGTGAGGAGGATACCGTGGCAGACGCGGCGGTGTTCTTGGACGCGGATGTCGAGGACGCGGGTGCCGAGGGAGAGCTGGCGGTAGATGGAGAGGGATTGGCACTGGGCGAA GGGGCGAGTGAGGAGAGGGATGCCAAS09155-1 TACTCATGGATCTTGTCCTAAACCTGATATGAATGATTCAAGC 70CCAACACGGGYGACAAGACTGATTTCGAGAGTGTGGACTGTAGCCAAACAGGAAGTGTTTGGTCWTGAACTTCCTATGGTTCATACTCATTTTTCATGCAATCTGCAATACGATCATCCTCCGTGAGATAGCCAGGCAGAACAACAGGATTGATGAC[A/G]AAACGTTGCAATTTATGCGCCTTGATCACTGGTTCGACATGCWGTCGTCAGTGAAGGTAGTTTGAATCATCGAGCTTCTCGGCAATAGTGTTTGGGAACAACTGAGATACAGGATTCGAAGGTACGGAAGCCATGGATACACAGATCTTGAATGATAACTACAAAGGATAGGCTCT CGATACCATATTTGATAAAACTGAS02037-1 GAAGGATAGCCCTGAYAGGAAGGGTGTCTTTACACGCTTTCC 75AAATCATGTTTTTGGCCTAGGGGATTGCTTTTGTTTTCCACATCRCCTTTCAAAAGCTCCTGGAATTTCCATTRGACAAGGCATAGGAAGAATTATCCATCAACAAAGCCCTTTTATACCCAGATTTGACAACATACCTTCCATGTTGTGAATGCTTC[A/G]AGATCAAATCATTACTAGTCTTGGTCCAACTCAACTAGATATTTTGAATAATTTGAGAGATATGTTATAGGAATAAAGAGTTTATGGAAGTGTTGTTCCAAGATTTGGACCCTGGCTCAATAAGGTCCTTAACCTTCAAAATAGGATCCATTGTAGAACCATTTGGAGGATCGAGAKAG TGCCTYGCCAGATTTAGAATYS13136-1 TTAACTTTGGTGGATTTTTAATTTTTTTAATTTGCTTTTCAAAT 80TCCAATTTGTGATATTCCAATTTGTATGTGTGAGGTTGCTTGTGTTTGATTGTGTTGAATTGAGTTGTYGCTTGCATTGGATGCAGTTGATAGGATGGTGAAGTGTGAGAAGTGGATTCGGGATGATGAAKATCACTTGGAGGGGTCTAAGGCGAC[A/G]TGGTGGTTGAATAGACTGATAGGGCGCACGAAGAAAGTAACTGTTGACTGGCCATTCCCGTTTTCTGAGGGGAAGCTTTTTGTTCTTACTGTTAGTGCTGGGCTGGAGGGGTATCRTGTTTCTGTTGATGGGAGGCATGTGACCTCTTTTCCTTATGGCACTGTAAGTKATATATATCTTT CTCCTCGAAGTTGCTAACC S17291-AAGACCCTTATGCACACCTAGCAACCTACATTGAGATTGTAA 84 001TACAACCAAGATTTCCGGTGTGCCAGAGGATGCAATTAGGTTGAGTTTGTTTTCATTTTCACTGTCTGGAGAAGCTAAGAGATGGCTACTCTCATTTAAGGGCAATAGTTTGAAGATTTGGGATGAAGTTATTGAAAAATTCTTGAAGAAATATTTTC[C/T]CGAGTCAAAAATAGCAAAAGGAAAAGTTGTCATCTCTTTTTTTCACCAATTCCTAGATGAATCCTTGAGTGAAGTTCTAGAAAGATTCCGTAGCTTGCTACGAAAAACTCTGACTCATGGATTCCCAGAGCCGATTCAACTTAATATCTTTATTGATGGGTTAAGGTCAYAGTCAAAG CAGTTTCTTGATGCTTCTGCTTS13139-1 GCTGAATGATATGATTCTAATAACTGTGGTTTAGACTTTACAC 89TTTGTTCTATTTCCATTTACTATTGTTTTTTTGTTCAAATCAGTTCCGAATTAGTGGATGCTGTCAAAGGTAGTGGTGATGCCATACACAAAAAGGAAGAGACTCATAGAATKGCAGAGGCAAATAGAGCTTTTGCACATTTTCATTAATTCATGAA[C/T]GGGATCTATATAGACAGACCCATATAGAGAGTATTTTGAAAATTGTAATCTGACAATTAATCTATTACCCTATTACTTCCAAGAAACGGGGAAAGATTTGCCTTGTTTGGTACTTACACCATAAATATCTTTTTAGGAAAAATTCTGCTTTGGTTCTTTTACATCTGAGAAGTGGATATT TGTGTTTTTTGACAATATTT S17292-TATAAATTTTCTTGTATCATGTTCAATTCTTATTGATAAAAAA 93 001AAATACCTCTCATCTCTATTTACCATABCCAAGTTGAAGTAWGGGGCTGTGCTAAATCTTATTTMTAGAGAATCAAGTATGTATTAATTGAATCAACTATCCATCAATAATTTCTTACCGTCTTTAACAATGTAATCATTTAAGTACATTATCCCAC[A/G]TTCTTTATTCAAATCATTTCATTCTTTTTCACATAACTACTTAATTATCCTATTTAACTACGTAAGCTAAAAATGTGTCCYGTCAAATAATCATTTTCATTATTATGGTTATTGGTTAAGACACCGACACAACACAGGGTTTAAATCTAGTTATGCAAAAAATAAAAATATTATTATTGCTT CACTCTTAAACTGACTTC S13146-1TGCTGCTAGTTATGTTAAATAGGTGATTAGGAAGTATTTGGA 98GAAAAAGGACTCAAAAATAGGCCAAAAAYTGATGAAGTTGGACTCTAACTATTCATCATGGCTATGATGAGTCATCATAGCCGCAATCAAACATAGGCATCATCAAAGTCGTGATCCTTTAATCATAGCCCAATGACAGAAAAGTTATGAAGTTCATC[A/G]AAGCCATGATCTTTTGATCACGACTCAACAAAGATTTGGATTTGAAGGATCATCATGAMTTTGATGAATCCATCCTAGCCGTGATGAGGACACGTTGGCAGTCACGTAACATATTTATATAAATAGCCTTTTTTAGACCCTAGGTTTCTAGTCTTTTATTCTTTTKCAGTTTTGAGA AGTTCTGGGAGGCAAGAGTGCTAS17293- TAGAAAACACATGACCAAATAAAACCATTAACCCTAATTCCT 102 001AAACAATATCTCTAATATATAAAGACCAACGATTTATAAAAGTAAAAATAACATTCAAAATTAGGTGAATAAAAACAATTTAATATAAAATTTAAATTATTAAACCTTAAACAATATCTCTAAAGCCTAAAGACCAACAATTTGTAAGAGTAAAAACA[A/G]CATTCGAAACTGAGTGAGTTAAAACACATGAACAAATAAAACCAATTTAATATAAAATTTAAATGATTAAAACCTAAACCCTAAATCTTAAAACTTAATCTTAGCATAAAATCACTTAAATCAATTATTAAAATCTAACCCTAACTCCCTAAAAAACGTGTTTGATGATTGGGTGA AGCCACCCAATTTGGCGCCACCAAS17294- AAAAATAAAACATAAAAAAGGATATATAATAAGTTGAAAAG 106 001TTAATAAGATAAAAAAATAAACACACTTGCTAAAGTTAAATCAACAACACATAATAATAATAATAATAATAATAATAAYAATAATAATAATAATAAAATAAATTAATTAATTAATTAAATACAAAAAGAGAAAGTAAGGAAAATTTCTAATTTTCATTG[C/T]ATTATCGACRTGATTTGTCTCYTGTGTGAATCTCAGCATTAAAGTTGATAGAGTATTTTCAATTACAATAAATAAAANAATTCAGAGTATAATTTGWTTTCACCCATAAATATAAARAGAAATAACTAAAATACACAGAARATCAGAAATATATTATGTAAATAAAAATGCADGA AGCAATCAVCAAGATAAAAATARAAS17581- AACAAACAAATACAAATCCTATTTAAAAACATTTTTTAAAAC 111 001ATAAATAACAAATTTTGCAAAAAAAAAATTAAAAACGTTCATACAKAGGAAGTTACACTTACGGATGAACTTCACCAGTACRAATGCAAAATTGGAAATGCGCAAATGCCATTAACGGAGACGTGAAGCTTACCTCGACGRTGGAAGACCAAAKCACA[A/G]CTACACGTCCTCAATGCCTATGGTGAATCACCCTATGTGACACGGACGAAGGAAGAAGAAGCTCGATCGGYGAYGAGAGGAGAAGAAGRAGGAGGTCGAAGGCGCTGCGGAAGGAAGAAGGAAGYGTATGAAAATAAGCTGGTGCGCGASTTTTAAATTTTAAGTGAAGGG AATTTTCGCCCATTCACTTAAAATGTTGGS17691- TACATTGGTTTAGACATTTGTGACTCTAGCTATGATCATTGTG 115 001TGATTGATTTGTACACAAGTTGAATAGTTAGCATGATCTTCCTTGCTAGTGATTTCACTGACATTAGTCATGCATATTTGTGAAGATTTGAGCTTGAACAATAAGGTTTTATTACACTATATATCTATG[CCTCTTTTCCTTGGCTATGTGATTAAGCTTCTCATCATTGTGGACTCTAGAATTTGTTTTGGAACCATGTTAAGATTG]TGTACTAGTTTGCATTAATGAAGATGATCAAGGCACATAGGAAAATTCTTTCTGGCCCTTGAATTAGTTGAGAGYTGTTGCCCCTTATTAGCCAAATTTGAGCCTAACACTCTTGTTATTTGGTACCTTTGCATTTGT TGAAATATTATAT S17701-GCCTTCACTTCCATTTCACAAATACACAAAAAAAAAAAAAAA 120 001TGCTAGTAGTGWAAACACTCAAAACACTCAAATTAAGCCCTTTCAACCTTTCTTTCTTATGAGTTTACAATCTCAAAGCCCATCAAAGTTCACGACCCTATTCATCTCTTCCAACATGAGCAACCCTTCAGATGAAAGGGAGCAGTGTCAAAAGAAGA[C/G]GAAATCCACCATATGCGAAGCCTCTAACTTTAGGACATCAAGGAGAAGATTCTGCAGCAACAACAAAAATGAAGAGGAGATGAACAATAAGGGAGTTTCAACAACACTGAAGCTTTACGATGATCCTTGGAAGATCAAGAAGACGCTAACCGATAGCGATTTGGGAATCCTAAGT AGACTCTTGCTGGCTGCAGATTTGGS03703-1 GTTGGAGGATCATAAACCACTTTTTTTTGCTAACAATGGTATT 125GGTACAAAGAAGCCCTGCCMGAAGCGGTGACTAATCTTCGTCRAAGACTATGAGCATACAAKAGATGAGTGTACGTATTCCCCTCCCAACRTGATTTATTCATACCCAAGGACTAACCAGGATTCAAACYATGAATCATTTGATTAAGCGACAMAAG[C/T]CGCTACCACTTGTGTCAACCGTTGTTRGTATCATAAACCACATTTATAAGCTTAATTAGACACCTTCTCACTCCATTTAATAAATTATTTTGAATATTACTTTTTATTAATATGTTGGTGTGAAAATAAGTCAATTGGTCAGTCGTGTCATCTTATTACCAACAAGTGATTTCCTTTAG GCGACTAACTCAAGAAAGAAAS17297- AKAGTACCAAACCATTTTTTTATACTTTCAAATGTTTCTTAAT 129 001GCTYAAATATATTAATTCAACAAAATAAAAAATAATTATTAWTAAGTAATAATTTTACAACAATATTTAATTTATTATTATACAGATATAACATATACAABTRAAAAGAAATAAATTAATAATTTCACAACACTATTTAATTTATTTCTGAAAAGCA[A/T]TAAACAACATTTTCACAACAATATTTAATTTATAATATTAAACATATCAGTTTACACACAAAAAAACTTTCTTACATATGTATTTGATAGTTACAATATAATATTTTTTTTCTAAAAAAAACTTACTTTATTATTAGTTGTATTTGCTAAACAAATATTTGAATCACGTAACTAAAAAGAA AAGAATTTGTATCTGTCGC S17298-AGTTCTTGTTGCTATATATTCGTTATCCTTAATTAACCACATA 133 001CGTGAAATTTAAAGATGCCATCACAAGCAGAGCTAAGCATGATGGATTACAAGCCCTACAGCTACTCHACACTGCTGAAATCATTTTTAGATCAAACTGAAACTGATCAGACCTACAAGCTTGAAGAGTTCCTCTCTCGCTTAGAGGAAGAACGTGT[A/C]AAGATTGATGCCTTCAAGCGCGAGCTTCCTCTCTGCATGCAACTCCTCACCAACGGTACAAGTTTCAATCAATCATCATCATGGTTTCACCAAAGAAACATATCAAACGTAGTTGATGATATTCCAAATTCCAATGAACCAATTAAAACATGGAATGTCCTAAACCCTAAAGTTTCA TCAATACCCCATGATGAAAATATS17299- CACTATAACAAAATTGACTTGTTTTTTTTTTAAATAACAAAAC 137 001TGACTTATACTAAGTAGGTTATATTTTGCTTATAAARAGAAGTAGCTTATATTTTAATCTTTCAACACATAAAACATTGTCAATAAATAGTAGAGGTGRCTTACACTACTAAAAAAAAAGGCCTTTTACATCGGTTCTAATGACTTTTCTACATCAA[C/T]TATGACGCGTGGTGGTAGTCCAATGTTGTCVAATAACGACATCGGTTGAAGGACCGTCTTTGAAGAACATTGRTACGAAGACGAGCATGGTACCAAACTCTTCTTAGAATGGGAATTGTTCTATATCGGTTGTGTAGGTACAACAAATGTAGAATGTTAGTTTTCTACATCGGTTCTKAGG GTGAAACCGATGTAGAATG S17300-GTCGGATGCTCTTATTTTACTCTTATTATTTTCCAGTATTTCGT 141 001TTCTGGCTATCCATATCAAGGAGATGCTAAATTTTAGAAGAATAGATATTGATATTATTAGTAATTATACTGGATGGTTATTTGGCTGATGAAATAGTCGGATACCCCTCCTTGATTAAAAAATAATCATATAAGTAGAGATGTCAAATTTTCGA[C/T]TAGTGGAATAGTTGAGTGTCCTTCACAACCCACTAAAAGACAATCTCAGACATCTAGCCACCAGAGTGTCTGAATACTTCCTAGAACATAAATGTCAGAYGGCAAGACAAATATAGACCTTGACCTTTTGGTTGGTCGGATGCCCGGATATGCATTTGGCCACCCGAATAATCAAATA CTCAATAAAGAGTAAACTCGACS17301- AATAGTATGCTATTCAAAAGTAGGTTATCGAAATGTGTTTGA 145 001ATGACTCATGTTCGCAAGGAAAATATCAGTACAAAAGACCTCAATTTACCATACAATTTGATAAGGGGAACAACTTAYAGAAAACATTATCGGACAAGAAAATTTGGATTAGTAAAGAATAACCCTATCACCTGTCATATACCCCTTTATAGATAGCA[A/G]GATCATGAGAAATACTCRGGATAAAGTATAGTCTAAGGAAACAACTTTATCTCTTAGCTTGGCAATATCTAACTATTTAACTATGCTATTTGTAACTAAATTGTGCCCTAACGRATCTCAAGGTCTTGACATTTCTCTCAACAATGTYGTCTCGAACTAATCCATACATAGCCTTAAA CTACTCACCATTTRAGGTGTCTS17306- GGATAAAGAAAATAAAAACATTTTTTTTTCTTTCTTTCTCTTTC 149 001TTTTCATTAAAGGCTATGTTTGACAACTAGCCGGAAAGCTAGCTAGAAATTAATGTTTTAAGAAAATGTAACTTCAAACAAAGTTACTAAAAAAGTTAAAACTTAATTTTTCATGTTTGATATGTATTTTTAAGAAACATGTTTTTAGGAAACTAT[A/G]AAACTATGATTCTTAGGAATAATTTTTAACTCACATTCTTGCAAAAACAAAAAATCCCATGGAGAAGGATGAGGGGTAGAATCTTACTTTTTAAAGTTTAATTTTTTGCTTCACTATAATAAAAACAGGTGCTACTCTTATTAAGTTATTCAATGTGGTAAATTTTAAAGTTATTGATAAA AATATCACGTAAATTTTTT S17310-CGATGATCGCAAAGTTTGGCTACGACAATAGCTTGAGTGAGG 153 001GAAGGTGGTTGGAAGGCCAGTACCTCATGGCGCAATTCTGGTGTAAGGCCGGAAATGGAGCAACTCATCAGGAATGTTGGAGCAAGGCCCACAATGCGATTAGCCAAGTGTTCGAATTCCGTGAGGTATTCATTGATGGTGCCTCTTTATTGCACTTT[G/T]AACAGAGCTCCTTGCGTATTTTCGTAGAAGGACGAGGAAAACTGAGACTCTAAGGCCTAAAGCATAGTTGACCATGACATGAAGAAGCCGTTGCGGGACATCCATGGGTACCACGAGAACGTTGGGCCCTCCATGTAAAAGGAGGCCACGGTCAAGYGTTCATGGTTCAAGAGAC CCTAATAATCAAAGAATTGTGATATS17311- AAAATTTGAATTCATCGTGGATTGGAAAGTATCTAGGGTATT 157 001CACAAGACCAAATGGAGTCGTGAAGTGCTCATAATGACCTTCGTKAGTGTGAAAGGAAATTTTGGGAATGTTAGATTCCCTTATGCGGATCTGATGAAATCTAGATTTTAAATCAAGCTTCGAGTAGACGCAGGAGTMATGGATCTTGTCAATGAGCC[C/T]CGTTGATGGTTGTAATAGGATACTTATCTAGGACAAGGACCTTATTGAGGGCCCTAAAGTCCACACATATCCTTTATGATTCATCTTTCTTCACTAAGATGATAGGGCTCGAAAATGGACTAATTGAGTGACGGATGATGTCCTTTGTGAGAAGCTCTTGCACTTGTCGCTTAATCT CGTCCTTGTGATGGTAAGCATTTS17312- TTGTTTGCAGYCGACAAGTGTACTGGATCGCACAAGTAGTAT 161 001AAAACGATAAGAACCAAGTATCAAACTCTTGGGGAACTTGTGTTATCTATCAAGCTATTTCGRTAAATAGGTGTCTGGTATGAAAAGATGATTGTGGTTATGAACAAGTATGTAAACTATCTATGCAAAAAGAAAGAAAATCACGCAACATAAATGTT[G/T]TGTAAAAACAAGTAGAGAACGCGTTGGTCTTCCTAATWGGTTCCTGATGCTAAAACGGATGTTCTCTATCTAACAATGCTCATGTATTCCTATGTTGTCTCCTGGACTGTTAGACCCCGATTCCTCATGATAGCCTAGCGTAATCCTGATCAAGTCTCATCCGCAGATTCCTCTTGTA AGACTAAACTCATTCAGGACCGS17313- AATATTAGTAGTTTYGTATTCCATTTTATTTGTTCTTCTCTTTA 165 001ATTACCAAACAACCAACCCCCCCCCCCMYCGTTACTGTTACTGCAAGTATATTATGAACATTTGGCTTGTCACTGCTCGTTGGGAAACGACCTAGGATCACTTCCTAGTTACTGCATTTTCATGTTTATTTGATTCGGGTACGGCCTCGATCACAC[C/G]CCCTCGCCTTCAGAGGACTACACGTCCTCCTCTTCAAAGGACTATACGTCCTCTTCTTCAGAGGACCACACRTCCTCCCCTTCAGAGGACTTCACGTCCTTGCCATCAGAGGACTACAYGTCCTCACCTTCAGAGGGATACACATCCTCACCTTCATAGGATTACACGTCCTCCCCTTCASA GGGCTGCACGCCCTCGCC S17316-TTCTRTTTTCAATAACGAGCGTCTCGATATATTACGVGACTCA 169 001ATCGGAGATCYGTGTAAAAAGTTATTGTCGTTTGATTTTTCTCAGAGCTTCAGTTTTCAATTCCGAGCGTCTCGATATACTACGGGACACAATCRGACATCCGASTTAAAATTTATTGTCGTTTGATATTTCTAAGAGCTTCCATTTTCGATTACGA[A/G]GATTTTGATATATTAYGGGACACAATCGAACATCCGAGTAAAAAGTTATTTCGTTTGATTTTTCTCAGAGCTTCAGTTTTCWATTTCGAGCGTCTCGATATACCACGGGACACMATCARACATMCKAGTCAAAAGTTATTGTCGTTYRAATTTGCTAAGAGCTTCTGTTTTCAATTACGAG CRCCAGCCCCACGTCATNN S17317-TCAATTATTTCAGCATGAAATACAAAARGATCTTCAGATGGG 173 001TGTTTCATAGCATCAAGAATATTAAAATGAACAGTTATATCACCAAACTCCATAGATAGTGTGCCTGCATATACATCTATCTTAGTTCTAGCAGTTTTCATAAAAGGTCTGCCTAGAATGATGGGAACTGATCCTTGAGAAAATCCCTCCTCCATTTT[A/C]AAAATATAAAAATCAACAGGGAAAATTAGTTCACCAACTCTAACTAAGACATCCTCTATGAAACCAGCAGGATAGGCAACACTTCTATTAGCTAAATGAATTACCACATCAGTTGRCTGCAAAGGACCAAGAGATAGAGAATTAAAAATAGACAGAGGCATAACACTAACAGAAG CTCCTAAATCYAGCATGGCATTGTCS17318- AATCTTAAATAGATAGTTAGAGTTTTTACATCAAGAGTGCTCA 177 001GTGGAAAAATTCTCTAACAATGAAGTGTTTAGCCCTCCATTAGCARGGAGGGCTCAATACAAGGTTGAAACAAGATAGAAATTGAGTGGTGAAGTGAATGTGTGAAGAAAGTAGCTTCCTTCAGCCTTGATGCTCTATTTCTTTTCTCCCAACCTGC[C/T]GACACTTTGTTTTCCCTTCCTGTTCTATTTTTAATGACTTTTGGGATTCTCGGATTATGAATGCGCACTCAGCCAGCATGTCTCGCTGAGTGAGAGTTAGTGATTAGGCTCTTAGCGAGCTTTGACACGCTAAGCGCGAGAAGCGACAAAGGCTTCGCTGGGCGGGCTGGTTGCGTGC TTAGCACGTTGCTCTCTGAATTS17322- TTGAATATTAATTATTGATAGTTATTAATAAATTATTTATTCA 181 001TAGTTATCAATTGATTTTTTACAATTGATAGTTTACTAGCTAGCTTTCTGCTAAAAACTGTTTGAAAGCAAAATGCAAATGCTATATGCTGTGTTGTGTGGTCTGATTTGAAATTTACAGGTTAAATTTTGGGTTTTTTTTTGTAAAAACAGAAAGT[C/G]TATTTAAAAAAAATCCTAATAACAACATCGATTTTTTTATAAAAAAAAGCCGATGTTAATCTACACAAACAACATTGGTTTTTTGGAAAAATCGATGTTAATATCCAAAARCGTTAACATCGRTTTCTGTGAAAAACCGATGTTAACATAGAAAATGTTAACATCGGTTTTCTATAGTTC ACATCGGTTTTTGACTGAAA S17326-GGGCAYGGTAAACAGCTGGTTAGTGAACTAGATTCTTGTTCT 185 001TTCTTTTCAAAGTGTTTCAAGATATCCTGAACTAAYGTAATTTGATGCTCCCTGTAACTCCCGTAGTCCCGCTGTATGBTGTGTTGAATTGCTTGCTCAGGCAGCTTGAAGGAGCACATTGCTAAGGTTAAAATAGCTGAAATTGCATTTATGGTGCA[A/C]TTATGCAATTTGCTGTAAGCAGTGTTGTGGTAGTAATGTTCTAAATCTTGAAAGTGTTGTTTCCTAGGTTTATAGCATCTATTTAAGGACTCATGAGAAATCCCAGTTTATTGGAACATGTTTGTCTCGCTGACATCTATCTGCTGTAGCATTCAACTAGTCTGTGTTTTGGTAACTGTGT GGACATGCCATTCAATCCC S17327-ATAGTGGATGTAACTAGAGTCTAACAGAGAGACTATGGTGGT 189 001TATAGGCAGTCTTCTTCNGCCATGTAAAGATAATACCAGTCTAATTGCTCCATAGTGAAGATGAGTGTATCCTTGGTGTTGCTAACTTCTGATCAGTTGTTTAGGAATCTCAATATTAACATATTGCTCCTCAAAAGTAGCAGTTAAAGAGGACTGGT[C/T]CATTCTTAAAGATTGGACATATTCTTTCATATGAGGTCTTCTAGTGGTGATCAAGTTGGTAATAGATCTTAAAGAGTAACGATGTCTTTTAAATATATGGTAAGGGCTCAACAAGGGATTTAGTGACTGAGAGATTTGAGCATCTTCTGGAATATATGAATATTCTACAAGATTCTCTATT TTTCTGAAAGAGTTTTGGA S17328-RTCTCTACCAAGAGATTCAGCAAGATCCACGTGTTTTGGAGTC 193 001CATAGATTCAATCHCATTTGTTGAAACTCCTTTGCATGTTGCTGCATCTCTTGGTCATTTTGAGTTTGCTAYTRAGATCATGACACTGAAACCTTMACTTGCTGTGAAACTAAATCCAGAAGGCTTCACTCCCATCMACCTTGCTTTACAATGCATC[C/T]ATGATAAAATGGTCCTTCRCCTTGTAGAAATGARCAAAGATCTCGTCCGAGTCAAAGGGAGTGAAGGCTTCACTCCACTGCATTTTGCAAGTCAACAAWGTAAAACTGAGCTTTTKGATAAGTTCCTCAAGGCTTGTCCAGATTCCATTGAGGATGTGACTACCAGAAGTGARACCGCA CTACATATTGCAGTGAAACAT S17329-ATCATTTGAGAATTATACTTCMAAGTTCAGACCTCATTTGAG 001GCACAAAATTTCKTGCTCCTTCTCTCCYTCTCCCTCCACTCATCTTCYCCTTCCTTCRAGCTCTTATCCAYGGCTTCCTGTGGTGGTGAGCTTYTTCTTGACTCATCTTCTCCTTGAAGTGGCRTCTCCAATCATCTTTCTTCCTTCTCCATTTYGCT[G/T]CCATGATCTTC 197AAGAAGCAAAGGACTCCATTGATGAAGAAGATCCAAGGCCTACAAGCTCCACATAGAGCTACATCACTTAGCAACTCTCCAATGGTCAATACCTGGATTACTCTAATATCTTCCTAACATTCCAACTRCAAAAGCAATGCCAGACCTTGTGCATACTTGAGCATACAT AAGGCTTCCAACAACTAAAGCS10746-1 TGGTTGATTCGAAGAACAATTDGGTTTTGATTAAYGTGATGA 202AGGTGTTTGCTAAGTTGGCTCCCTTGGAACCTAGGTTGGGGAAGATTGTTGAGCCTGTTTGTGACCADATGAGGCGCTCTGGGGCCCAGGCATTGGTGTTTAAGTGTGTTAGGACTGTGCTCACTAGCTTGAGTGATTATCATTYTGCTATTAGGCTC[A/G]TTGTTGAGAAGGCTAGGGATTTGTTGGTTGATCAGGATCCCAATCTTAGATATCTTGGTCTGTAGGCGCTTTTGGTTGCCACTCATAAGCACTTGTGGGTGGTGATAGAGAATAKGGAAGTGGTGGTTAAGTCGTTGAGTGATGATGATTTGACTATCAAGATCYTGTYAGTRCGATT KTTGATGGGCATATATGGTGTCS17331- TTCATTGGAATGGAATATAACAAAGTAATTAGATTAGATAAG 206 001AARAATAGTTGGAAATGAGACGTTAGTGTGGTGTGCGAGGCGAGGCCATGTGCTCCAATGCGGCGGTTATTTAAATATGTCGTATTGTTTAGKTACACACATTAACGTCAAAGTTTCAAACTATATGCGGTTGTCTCYGSTCTTCTCAGATTCTCTCC[C/T]ACGATGTTATTAATTGTCTTCATTTCCCATCTCTATTCTCTATTTGATCACACCGTTAACATGTTCCCATTCCATCTCATTGACAATACAAAATAAATTATTTATGCACTGAAATTAATATCTTAACACACATTTTTATTTTTTTGGTAACGTCACACATTTTTATTTCATTGTAAATTATCAG GTGTAATAAATTTAWT S17332-TCCAAAATTTTAAYAGTTACGATGAACARACTAAGCGCAACA 210 001GGCGCGYTTAGCACGTTCATCGCTATTTCCAAACAAAACCACAGGGGTYTTCACCCGTTTTAGCCACATGGCCCCTAATGGGCTTCTAAGTTACCTAAAATCCTATATTGACTAACCCTAAAACTAATAACCTTACCCTAACAACATACAACTAAGAA[A/T]ACAAGAAGTCATCTATCCTAAGGTTTGAAGAATGAAAAATGGAAATAGAAAAGTACTCACTTACTTGGATTGTTCTTGAAATGAAGCAAAGAAGATGYAGACAAGCAGTACACACACAGCAAAAATACACACTTGCTYAGGGTTCACAAATGTAGAAGCTGAAGGTATTTGGGGT AACACCCAAGATCCTTAGCCTTTGTS17337- TAGTCTTGTTATTTTTTAATTGAGACAATTTATTYCCAATTTTA 214 001AAAAGTTTATAATTTTARTCTCCTATTTTTTAAATTAGACGTTTCGTCTTTCACTTTTAAAAAAATCAATAATTTTAATCTTTATGTCCAATTTCAAACGTTGATCTATACACTTTTGTAAATGTTGATTGATAATTTTTTTTATTATGTACATGA[C/T]AAATATTTTTTTTATAATTATTTAATTGTTATCAAGCTTAATTTATTAAAAGAATTAAAAAAAGTCTTAATTAATATCACGGTCAATAGGTTTTAAATTGATCAAGGAGATTAAAATTATAAATTTTTTTTTAAAAATAGAGGACGAAATGTTACAATTAAAAAAAATAAGGAGACTAAAATT GTATATTTTTTWAAATG S13093-1TAAACACATGAATTTTTTTTATCGACAAATATTAATCATTAAT 219TTGTTAGTAAGAGGATMGAACTGCGCSATATTTTTCTTGTTCCGTTAAATTANACACATGAATTAATATGAAGGGAAAATTAAACAACAACATGATACATACCTCAGCATGCACAACATGAAGCATCGAGTCTCCAGMARGTGAGGAATTGGCACTT[C/T]TAACATCAATGTTCTCTTCATGCAGCATTCGAATGATCTCAGAGAAAATGAACTGGTGGTCTAATCCACAAGTAAGAACAACTTGTAAAGAAGAACCCACTTCGTGAATCTCAAGTTGTGGCGATTTTGGGAAACCTGCAGAAGTTGCAGCAAAATTGGTACTATTATTGGAGAAGC AATCACGGGATCTCTTTCTAATTS12211-1 TACTAGACACTCACTCATTGGATTATGAGTATTGGTATTAAAT 224GTGACCATCACTTACAACATTTAAACTTATGATAGTATTAAATGTGACCACCACTTTCCTTGGTCTTGATGATTTGTCCTATATTTCTTATATATAGGACCAGAGGTAGTAGATTCCAAAAGTTTATGCTACCACAATATTACTTGTAAAGCTGCAA[C/T]GCCATACTAAACCATAATACATAACTGAGTGAGCTTAATGCAAATTGCTTGTTCACCAGAAATAAATAGAAGATTCAGGCACGCGGTACAACAGGATAATGGAGTCAAAACACAAAACTAAAGTTATTTATAGACTACCATGTATTTTATTAAATGACCACTAATTTGTGATATAGGCCA TTAAAAAACAATTTCATCAAS04555-1 CTTCAATGGCATGGCCGTGGAAAGAAACAGAGCTTAGATTCT 229CTGTTTTTAATTCTCCAACGAGGAAGCTCCGATTCGAAAATTGCCTCCGCTAGGGTTCTGCAGTTCATCGCCGTGGACGCGGATGCGAAGATYTCAATCGYCGAGAAGCAAGGCGTGGTGGCCGAGTTGCTGAAATCGGCCGCACCAGAGAAAGATCC[A/G]GTGCTGATCGAGGCCGCGCTGGCAAGCCTAGTGGMGATTTCGGTGCCGAAGCGGAACAAACTGAAGMTGGTGAACCTCGGAGCGGTGAAGGCGATGAAGAGGCTGTTGAAGGAGGCGAATTTGGGCGCGGTGGAGAAGGTGCTGAAAGAGAATGAGAATGGAAGAGTGGAC GACAATGAGAATGGAAAACTGAGGGTAGAS08519-1 TTTGAAAGAARAAAGAAAGTGCTCACTGCTACCAATATACTA 234ATACCGAACCATCCAACCAAATTATCTTTCGTCTATACTTTTTAGGCTTCACACTTGAGGAGGTGTGAACTGTATGGCCAAATTCTATCAACAGACCAATCAAATATTAACCCATAAATGGCTCACCATGTCCAATCAGGCTCATGGCTGATCTATTG[C/G]CAGAGCTGACTCAATGTCAAGGCCAATGAACTGTTGTGCACTGATAGCAGGAAGACACTAGAGCTGTGAAGAATTGGCAGGCCAACTAGTCTTGGCGGCCCAACDTAACAGTCTCTTGATCCTTCTCATGGATCTAGCTAAAGTGTCATTGGCCAGAACAGTTAAAGAATGGCACAC TTGTTAAATAGGTGTGACTAGTCS12876-1 GAAAGGTCTTCCCCTGGTTCATTTCCTTGCTTCTTGGCTGACT 239CACGAGGACTTCAATCGTTTTCTGCGAAGCTCTTAGGGTCGTGGCTCGAATTGGGATCAGGGGATTCTCTCTTTCTCCGATGATCTCCAAAATTGGAACCGGGAGGTGTTTGGCAATATCTTCCGAAATAGGGTCTCCTTAAGCAAATTCAGAGATT[C/G]GAAGCGTGCTTGGGCTCCTCCTTTTCTGATGATCTCGTTTACAGATAACAAGAGTTGTGGCGGGAATAGGAGCAAGTGCTGATACAGGAGGAACTATTATGGTTACAAAAATCTTTTTGTTACAGCAGGGGATTTCGTCCATTTCTATTTATCTAACTCTTTCCCTGAGTTGGACATGTTG GCTGCCAGGCCAGCTTGGTS05937-1 GAAGGGGGCTGGGTTGGAGTAACACAAGGGGAACTCATAGT 244CAGGCTTGATAGACCATGCCCAAAGGAGTAAGGAGAAGAATTAGAATYCAWGTAGAGGAAATTATTGAGAAGCAAACAGGAAATGGCAACAATTGAATTGTTCCCATGTCCCAATGGGCAAAGTCCAGCAAAATTAAGGAGAGGACCTTGATAATCATC[A/C]GCTATGACCATGTGCACTGGTGCATTTTGCAAGAGAGCCAACTCAGCCAAGGGATCTTCACAATATAACCATAAAGGCTCTAATGCTCTGTTTCATGACGAACTGGAGTCGGAGGTGGGCTGCAGGGTAAGTTTGAGTTAAGTCACCAACAATACCATGAAAAACAAAGGC GCTAGGGGAGCAAGGGCGTTCACATGCTTS08575-1 GCAATTTGAGTATAATTAGCTGCTTCTTTGGACATATGTTTGT 249ACTGTGTGTTTAGTAGTGCTTTCACCAGGTCCAATGTGCATCAAAACAGAAGCAACTAAAACTAGCTTCCACATTTTTTTAGATGATATGAGGTGATTTAAGCTTCAAACATGCATATTTGGAGTGGATCCAAACATGCGTCTAGTCTAAGAGATTC[A/G]GCAAGAAGTTCAAAGAGATGAAGCTCTAAATTTATTATTTTTGTAATATTCAGAAATTAAGCTTATTACCATGAGCATAAGTGCATAGTTACAACAATTTACTGAGACCTCTTTCATTATGGTTGCTCATAAATGGAATAACATTTTCATTTTTAATTATATCATGTTATTCTCWACATC TTCCGATTGCTTAGTTTGAAS08669-1 CCTCCATTCATCTAGATAAAMAGTTGAAGTTTAGCACAAGGT 254ATGTTATGCTTGTACATTGTCCACACTTCAAGCCCAAAACGTCTTGCATGAGGTGGTGGGTTGGTTTTTGACATATCATAATATGTGTATCTTGTGCTAACTGATCAGAAACTTCATTACATTATCTGTTTTTTCTGGGTCATTTTCTTATGGGACAT[C/T]TCCTCTAKGTCCTCAGATCTGAAGAGGCTGAGAATATTGGATATGTGATTCCTACAACTGTTGTATCTCATTTTTTGACCGATTATGAAAGGAATGGCAGGTATACTGGTAAGAAACTCTTCTAGAATATGGTTATATTTGATAGATTTGGCATGTCACTATGTCTTATTTGAGTAAGCACA CTGGATTGTGTATTTTTT S11212-1TAGTCTTATAAGAACTTCAAGACTTGTTTCTTTAAGGTGACAA 259TAAAKTCGATTACTGGGAATAACTTATTCTTTGATTCAAAGAAATCCTTGTTTCCTTTATATAGGCTKCCATATCTGTGTYAGTATGATGAATACCTTAAGGATTTTTTTTASCAAAAGGAGCTCCAAGACCTTGCCTTCCTCGAGACCCTCCCCCG[G/T]TTACTTCCTGTTAAACAAATATTTTCCCTCCTTAAGTCTCCTAATCTCATTTGGGATCTTGAGGGTTAGTTGTTTTTCTTTTGTGCACATBTCATTTTTTGCCCAAACTTTCTGATTTATTATTTTTGACTTGTTTCAGGTATAACGACTCAAGCACGCGCCAACATGACTGCTTTCTAACTTGC CCACAAAAACTGTAT S00543-1CTTCAATTGATAAAGCATTTGCAAGCTGTGAATTGAAGTTGC 264AAAACCACAACTTCATGGAAATCCTTCAAGAAAATAAACTAGAAACTATGAATATGTAGTAGTAGCAGTGTTAGTCAGAATAAGTAGCATGCAATATGAACAACTTGACAACACACTATAAACATAAATGATAAATAACTGACTGTTCCACTTATCCA[G/T]TGGTTCATTAATATCAAATATCAAACATCTTTGACAATTATTAGACATGCATACTCATGTGAAAAGGGAAAGGTAATTTTGATGTTGAAAATATRCAGAATATGTATGTATACTACATACCATGGTTACTAATTACTATTTACTATCTACGGGATTGTAGGCTACAGCTACTATTGTT ATACTCCACCTCTAGCTGAAACS01452-1 TTCAAACCAACTTAGSAGCTTGAAGCTCAAGAATAGGAAGAT 269AGGTCCCCAAAATGGAATTGAGTGTRAAGTAGAAACTGAAAATACATTTGATGGTGTTTTGGATCCTTCTGTTGTATGAGCATAAGGATGCAGTCAAACAATGAATGATGAATCCAATAGCTATAAGAGGAWACAAACATGTGGCATATGTGAAGCAA[C/T]TGGTCACAACAGACGAAAATGTATTGGTGGCTCTCAAAATGCACAACATGCAGTTGGTGGGTTTGGTATTCCTTCAAGTCAGCAAACATACAATGCTCCTAAACCTACAGTTGAGTATAATTATCATCTGGTATATAATTGCTTACTTTAGCCTCATTAATTGTAAATGGTTGTTAT TTAATCAATAGTTACTTAAGTACS11993-1 CATCTCATTCTGAATCTTGCGCCGTTTCCCTCTCCCACTCGCC 274AGGTACGTCATGTMGTTTTTGCTTCCCCGTTGTTGCGTCGATACGACTTGTCGTTTAGCACGTTCATGTTCATGTTCGGTTCGTGTGTGTTGCAGTGAGGTGATTTGATTTGATTTGTGAGTGCTGCGGANTTTTTTTTTTCCATTTCCAGCACAAT[C/T]GATTCGTCGGTACAACTTGTCGTTTAGCACGTTCATGTTCATGTTTGATTCGTGTGTTGCATTGRTTTGATAGTGTTGCGGAATTTTTTAGAAGTGTGAATGTTCGTTCATGCATGAGCGGCTCTTAAAGTTKCCTTGCGGATTCGATTGCGATATATTGAGACTGCGATGGCCTCAGCCGTC GTGAATTTCTTGAACGC S13446-1GGGGTTTATAAGRCCTTAGACTTTCGAACTACAACAGCTAGC 279ATCTATGGTGTGATTCTCCGAAGTTTAGTTTTTGGGGTGTGATTCTCCTAACCGAACTAGTCAAACAACTATTGCACAACCAGCCTGCATGGGCACGGGGCTGCGCTACTTTCGTACTCAAGCCTTCTGATACTGAATCCTAGATTATTCAATCTGAG[C/T]GTGGTGGGATGTTAAGATCCAATTTCAAGGTATGGTACTTATGTCCCACATTAGAAGCYTGGGATTCTAGAGTAGGGTTTATAAGGCCTTAGGCTTTCCAACTACAACAACTAGMATCTATGGCATGATTCTCCAAAGGTTAGCTTTTGGGGTGTGATTCTCCCAACAAAACTAGTCA AACGGCTAGTGCACAACCAACCS00252-1 TTTGTAAGAGAACCTAATTTTTGACTATAATGTGCTTGAATTT 284GATACATATATCTTATTTAAGGAAGATCCAAACTCATATCAACCACATGTTGATTATATAACACATAATTAAATAATTAAGTGGATGGTATGAATTAGTTTTGGTGATGGCACATGTATGCATGCAGCTGGGCAATAATGGATGGGGAAGCGGTCTC[A/T]TGGTACTATGATTCAAGCTCCCCGGACGGCACCGGTGCTTCTTCATCGGTGGCATCTAAGAACATTGTCTCCGAGAGGAATAGAAGGAAGAAGCTCAACGATAGGCTTTTGGCACTTAGAGCAGTGGTCCCCAACATTACCAAGGTACTCCATCACCTTAATTAATTAAACTAGCAA TTATTATTGTTCATCATATATTTS04060-1 GCCGCCGGAACTGCTTCGGACTCCCTCACTCTTGGAGCGACTC 289AGGTCCTTCCATAATCTTTCTCTCCACAAACATGTCCAACCCGAGCCAGAGCCAGAGCCAGAACCTGAACCTGAAAAGCCGGAACTGGTTCGGAGTCCCTCGCTCTTGCAGCGGATTCAGTCCATAAACTTCTCCCATCTCTACAGATCCGACTTCA[C/G]TCACCGAGATGATGAGGATCCSGATTCGGGTTCGGATCCGGGTCGCGGTTCGGGAAAGGCGGCGGAGATGAGGAAATCGGCGAGCGTGAGAGGGGGTTTGACGGATAGCGAGTGGGAGGAGGTCGAGAAGCGGAGGCCGCAGACGGCGAGGCCGGTTGAAACGACGACGTCGTG GAGAGAAGACGAAGAAGTAGACGCCAS02664-1 AATCGTTTACAGTTGTGAAAAAACTGCATTGGTCCTTTAATTT 294AATTTATAAAATGATAAATATATCTTTAGAATTTAGTTTAATRAATTCTAAGGATGAGATTTAGAACTGCTGCACATTGCAGTTCATTTTTAAACTGCAGAGGTCCCATTCTCTGTAAAAAAAAGAATTTTCTTCCTCTGCTATTCCTTTCYATCTT[A/G]TTCGTTCATTTCTCAACTAGTTCATCCTAAGGAAACCAAAACTACTAATATATGAAATGAAGGACACTATATAACTAAAGAGACATATGWCGGACCATTTTTAAATATATAAAACTCTATTAGAACTGCTAAAGTGAAGATCCTTATTCTTTGCCTACAAATTTACTTACGTACAATACG AAGGAGGAACTAAAGTTTATS00281-1 AATTTTCTTGCTACCATACCCAAATGGATTGGGAGGTCCTACT 299TTTTCCTTTTCATTGAGTGACATAGAGAAGAATTTGAAGGCTTCATATTCCAATTCGGATATAGCTTCCATGGAGACACCATGATTGATGACTTTGAAGAATCCAAACTCCTCACAAGCCTTCACTATAAGGGTCTTTGCATCAGGTTTGGAGAGGT[C/T]CACTATGGGAATTGTTGAGGAAAATTTGGTTGGCATGCAGTTCTTAATGTAGGAGTATTGTTCTGTTGTTGCTTTGGACAACAACACCATTTTTCTTGTTGTTTGCTCGGCCGTTRTTCTGTTTTGTGGTGTTAAGAAGTGGAGTGAAAGATAGGGAGAAGGTACGTGAGAGAGGAACAGA GATATTTGAAAAGCTTTTG S01109-1GATTCTGGTGACCCTKCTCTCGGTTCTCTCTTCTGCATCGTGT 304GCACGAATGGTTGGGGGGAAGACGGAGATCCCTGAAGTGAGAAAAAACAGGCAAGTGCAAGAGCTTGGAAGGTTCGCGGTGGAGGAGTATAACCTTGGTTTAAAGCTGTTGAAGAACAACAACGTCGACAATGGGAGAGAACAGTTGAACTTTTCAG[A/C]GGTGGTGGAGGCGCAGCAACAAGTGGTGTCAGGGATGAAGTACTACTTGAAGATCTCTGCTACTCATAATGGTGTTCACGAAATGTTCAMCTCTGTGGTGGTGGTCAAGCCATGGCTTCATTCCAAGCAGCTCCTCCATTTTGCGCCTGCATCATCATCCACCACCACCACCACCA CCACCATGCATCCAGTAGTACGTAS13844-1 GCCACCGTGTTTTTTAAGATCTGTGCTCATTAAGAAAAACAA 309AGCAACTTGMTGAAACCTTTTATCCACATACATATATGGTTAGTTAACCTTAATCCCCATTGCTCAAGCAGATATTAAATATTCTTTGTGAGCACTGAGCAGCCCTCATATGTTTATGTACTGAAAGATCAATATTACTTGTTAGTGATAAAGACTAC[G/T]TAAGGGATAAGAATGAACATAGCTGCAGGAATATTCTTGGTTTTTTTTAGTACTGCACAATTAATTCTGTATTTATGTCTCTCTTTAGTCTTTTTCGGCTTTCCATCATGCATATATCTAATATTTACTTTAAATTTATTGGTATCTTTTTTTTTTTACTCTTCCTGAATTTTATATTTCATAC ATTCTTTTAATTAAAA S05058-1CCCTCAATACAGAGCCACTGGGCAGATACTCATCCATTTGAA 314GTTCTCCCGACATTAATAGTGGATCTGTGAGTTTCCACCATTTGAGTTGTGCTATATTATCACCATTTTTATCTTTTGACATGCTATTATTTGTAAATCAACCAAAAATGATACGCAATTTTGACTCAGAATTGTTTAGACCAATTACTAATATTTGC[A/G]GTTCATTGTACTCCAATATTTGATAAGTTTGATTGGTAGGCATAACACATTAATCAATGAAATGGGGTGTAAAATACAACTAGATTATAGGGACATGTAACTTTCAAAGTGTTTTGAGTTAACCTGCTGTGACACTGATCAGCTGAACATGTCCTTTTTCTAGAAACTAGAAATACAATTGC TTAATGTCAAAAACAAGA S04660-1ATTGGAAGGAATAAAGTTGGGGTTTTGGAAGCAATGGAGTGG 319AATTCATTCCATTCTAGTTTAACAAATTCAAACAATGGAACATATCAAAATTCCATTCCATCCTACTCCATTCCTTCAATTTCCCCATATCCAATCACATTTCTCTGTTAATAGTTTGGGTGCAAAAAGATAGATCAAAGAAGTAGATACAGGAAGGA[C/T]GTAGATGCAGAAATGAACTTCTATGACGAAGGCYGAGGCAGGCGGCAACTAAGTGAGGGATATGCCTTAGTAACAAAACAAGGAATTAAAACTTGGTTTATTTTATTGGTAAAACATTGGCAACATTTTTCTCAGCCATGTCCATGTAAATGTGCATTTGTAATAAAAGAGTTTGGT GTAGTGGAGCATGGTTATTGTAAS09955-1 GGGTCAGATTAGAGAGTGAGATAMAGTGAGAGGGACTCATT 324TGAGAGGAAAAAATAGTTAAAAATCATTGAGAGAGAAAGGAGAGGRAAAATCATTRTGATTTTCGCATACCCACTAGAGAGCATTTTTCATATTGAAACARCAGATTGGTTCACCGTTGGATCGGGATGATTTTTGGAAATMTGGTTCAGCACACTTGA[C/T]ACTCCAAGTTGTCTGGTTGGATCATGAAAAGATATCTGGAGAGAGAGATAAGTKCTTCATATTCTCTGTTCTATATTTTRGGATTTCCTCTTCTTGTCTCTATTGTATCAACTCAGGGTCTGTTTTGATTTGGCTGTTTGTAGCACATTTTAGTGTACTTGTTGGAGGCTCTCTTGTAT CTTTATTGATTATAGTGGAGTS08034-1 TTGAACCAATCAGATGAAAGAGGTTGAAACTTTGCAAGACAA 329TGGCGAAGAATTGCTATTCCAACCACGCCTTCAKCAACATCAGTCAAGAGGCTGCACAATGCTTGCCMTCTGTATGTAAGAGATTCCTTTCTAAACCCTGCTGTGTATGCTAAAAATGGAACTATCCAAGATCCTACAAACCAAAATGAGGCAATCCA[C/G]AGGAGCATTACCTGCAGAACCCAACTTAGTTTGCTCTTCTAGATGAGATGAAACTAAGAAAGAGACCAATCAAATAAACTATATAGTTTCTGAATATTTTTCAATTCCATCCATTCACAAGTTCTTAATTGAAGYAGACTATAACAAATAGCCTTACTGTCAAATCAATAAAAAAAT TATAATAAGTAACCAACTTTTAGS10293-1 TTTTTGTATTAGAATCATGAAAKTGTGACTGAGATTTTGTGTA 334AATGATAAATTGAATATGTATTGAATTGTAAGATACATGTGTATTGAGATGTTGTGTGCATTGAGTTGTAAGCTATGAACCGTACAATCACACAACTTTAAGACCCTTTAAGGGRGAHGATTTAATGCACGACGAGTATTGTGATGAGATCGACTGT[A/G]GAAACCCCACGAGTTTAATCACTTTKAGGCARGACRAGTTAAATTTATTTTGAAAATAATTGAAGAGTCGTGTGTTTTGTATAATTCATAGATAAAGTCTGGATGCCCAACGAAGTTTTTTACTGACATGATACCATATTGCATATATGATTGAGTCTTAGTATATTTGTTGCATAAC GCTTGTGTATTGATCGATATTGS03813-1 GTGCTCATCAYGTGTTGTGCATGGAATGGCAGAGTTGAAGAA 339TCTCTTGAACTTTTCAGGGAGTTACAGTTTACTAGATTTGACCGGAGGCAGTTCCCTTTTGCTACCTTGTTGAGCATTGCTGCAAATGCTTTGAAWCTGGAAATGGGTAGGCAAATCCATTCCCAGGCTATTGTAACAGAAGCCATTTCAGAAATTCT[A/G]GTTAGGAATTCGTTAGTTGACATGTACGCTAAATGTGACAAATTTGGGGAAGCAAATAGGATTTTTGCAGATCTGGCACATCAAAGTTCAGTTCCATGGACAGCCTTGATCTCGGGTTATGTTCAGAAGGGACTCCATGAAGATGGCCTAAAGCTATTCGTTGAGATGCAAAGAGCC AAAATAGGTGCTGACTCGBCCACS02042-1 CCTTGTGTTCTCTAAGAACTATGCATCTTCTTCGTTTTGCTTAG 344ATGAACTTGTTAAAATCATGGAGTGTGTTAAGGCAAAGGGTCGGTTGATTTTTCCCATTTTTTATGATGTGGATCCTTGTCATGTGCGGCATCAGTCTGGGAGTTATGGAGAAGCGTTGGCTATGCACGAGGAAAGGTTCACAAGTAGCAAGGAAA[A/G]CCTCAAGGAGAACATGGAGAGKTTGCAGAAATGGAAGATGGCTCTTAACCAAGCAGCTGATGTGTCTGGCAAGCATTACAAACTTGGGTATAGTACCCCTCTTCACGAGATTTTCCAATACAATCACGTGTTCATGGTCCCGATCAATCTCCACGTGACATAGTCAAGGTCAAGATTGG TCGGGACCATGATCACTTGGT S16601-CAATCCCAAYAGCCTGCTYAAACATAGAAATAAAGGAATTTT 349 001ATTTGAAAATTACTTATTTTTCAGCCTTTTGAAAGAAGTTTTGAAAAAAAAACAAACTATTATTTCTTAAAGGTAATCTCGTACCAAACATAGTTGYATTGTATCTGAWTTCACACATGTACTAGGCTTTGGCAATGCTCACAGTCCAAGCAGCTTCA[A/C]AACATTTACACCCTGAAGCATGTGGCAAGTCAAGCTGTGTGAAAGGTGGAATAGCAGTGATGTTCTACACATCACTGTGCTTGTTGGCATTGGGAATGGGAGGGGTGAGAGGATCCATGACTGCATTTGGAGCTGACCAATTTGATGAGAAGGATCCAACTGAGGCAAAAGCCCTTG CAAGTTTTTTCAATTGGCTTTTGS01481-1 AGCAATAATTCTATGGCTTTTACTTTATTTTTTAGTATAACTA 354AAAAAAAAAGAAAAAAAGCCAGAGGCTACACCAGCATACTTGACCAGAGATTTAACTTAAGCAATAATCATGAGATAAATGGTTTCATCTGTCCTATATAGCAGCTYAAGCTTTCAGGCTGGCTGTTTCTTTGACATGACCATAAAGCTTCAGTCAC[G/T]TTATGGTCCAAAGTTTGACTTTGGCACCCAGAGTAGAAATGAGATCGTTTATCCTTATCTAACATGCAGTTTTAAATTCAGTAGTCCTTTRWATTCATATTATATATAGCACCAACAAWGGCCATGACATAGGAGATGGGAAAATACAAAAAATGGTGAAAGTCTATARCAGCMTAA AATGGATTCATTACCTTCTTTCTS11309-1 GTTTAGTCAAGAAAAACAAAAAAAAAAGTAGTAAAAAATGT 359TTTTAATAAAGTGAGAGTGGAAATTATTAATCGTGTAGATTTAAAAATAGTTTTAGTTATCATGAAGAAGTAACATATATGGATAGAAAGTTAAATAGAACTGGATCGGCGTATATATTGGGCTGGACCGGTCTGGGACAATGATTGGGCTCCAATTTC[A/T]TGGTTCTCGTTCTTCTWGGGCAACTTGATTAAGTGATCTAACTTGTGGATAAAAAAAGAGAAAATAAATAAAAATAAAATTAACAATTAAATGTAAAATTAAAAAGTGTAAAAGATATAATATGCGTTTTTATTTCTCTTCCATAGAATTTTGGTGTATATAATGGCGACAATAAGG TTCAAACCTAAGTCCTTTCTCTTS11320-1 ACTATAGTTTTTATTTTATTGCGGTTGTAATATACATGTTTTGG 364TTAATTTTTAGATATCTGCTCTGAGGAATTAAGTGTTTCTCAGTCTTTTGAACTGGATGGTGTAATCTCACTTTTGAATCGGATGCGAATATGAAGTGGTATTTGGATTATTTTTAATGGGTTGTGAATGAAAATAACGTTACCTGTTGAGATCGT[A/T]TGTTTTATAGCGATAGTGTTTCATAGTAGTGTAAGCTGGCTTACATTGCTTTTGAACTTTGGGCGGTCAACTGATGGTTCTATKTGTCTCGTATGTATATGGTCGATCCTTTGCTGTTAATGCGGCGTGTGCCTTTGGTATGTTGGTTTTYGGGTGCTGCAATTTGTAGTTTCTTGGCAATCTC GTCGATGGTACTTCAA S04040-1AACTGCAAAGGTTCAAGTAGATACYTATTGGCCAACCTTATT 369TGCTAAACTTGCTGAGAAGAAAAATCTTGGCGATTTGATAGCCAATGCAGCAGGCGGTGGTGCACCAGTTGCTGTTGCAGCTGCCCCTGTTGCTGCCTCWGGTGGTGGTGGTGCTGCTGCTGCCGCCCCAGCTGCTGAGGAGAAAAAGAAGGTTTCCC[G/T]CTAGTGAATTTGTTGTTCCTCCAATTGTTTTTCAATCCTGCTTTATGCTAGTTAATGTGTATCTAATATGAATCTGTGTGTTTCTATTCTATAGGAGGAACCTGAAGAAGAGAGTGATGATGATATGGGATTTGGCTTGTTCGATTAGGGACATTCTCAATATGATTTGGTTAAATT TTGTGGTTCTTTACCTTTAAGTTS00863-1 TGTGCTCCTAGAGGAATATTTTGTGTAGACTTTCTATTATCTTT 374TATTTTTTCATTTTTTAAAATTCAAATGTTAACAATTCAAATAAAGAGAGAAACTAAAATTTCATAAAAGAGAATACGTGTATTAATTYTATTTTTGGTTGACATGACTTTTTCATACTAAGTTGGACACCAATTGTGTGTGAGACTTATACCATC[A/T]TGTGAGTGTTGAACATTCTTAGTGTATAACACTGATAATATAAAGGGRTAGACACTTTTGGTCTTATAGCKTGTGTGATGCTGATTAATAATTAACAAAATATTTTCTTTTTTGWGTGTGGATGATATATGTGAATAACACTTAAGTCCTTTAATAACTTTGCTCACGTCCACTTGTCATAA ACTTATTAATATATNAAA S17151-ACGTTACCCTTGCACTGCAATGCGTCATTAGATTTTATTTTAT 378 001TTTNTTTTATCTRAAATAACTCAYAATAAATTTTACAAGTTTAGCTACGGAGAAGATAACTAGATAAAGGAGCGATTGATGTACATTTTGAGGGTGTATGTAGGTTGGAAAARGAGAGGCATGAGGGGGAAAAAGAAGAAAAAATTCCACTAATGTG[A/G]TATGAAAAAAAGAGTCACAGATTGACTGAGACTYGTCCCAAACAAGCATGTTAATCCTTGCAAATGCGTAGACATAAACATTTTTTTAGTTAATTACCTTTTTCATCTCTAGAGCTACAACAACTTTCTCATTTAATTTTTATAGTTTAAACATCTCATTTTAGCTCTTATAAGTATAT AAAAAATTTAATCTTTTTTATS17153- TAAAGTTYAAGAAGACACATGTTAWTTAAACATATTAGTTTA 382 001AAAWGTAAATTACACTAATTATCCCTAAAGTTTTGAGAAATTACACAAATTTCCCCTACTTTTATCTACTCCTACACTAACCCCCTAATTTTTTGAAAATATATATTGATACACCTTATATACAACAATAACTGCCCTTAATTGCTCAAATTTCCACT[A/C]TGAGCCTCTTTATCAAATCTCATATTGCATTGTCACACTCCACGTCAGTTGCAATCACTCACACCCCTCCTATATAATACATCTTCACTCTTTGCATCCTCACCCTAAACCAAACCAAATCGAAGACAAAACAATTTTAACATCAATCTCAAGGGTATYTTTCTCTCTCTTTTCTCTTTCCT TATTTAGTTTAATATATA S17154-AAATTTTGCATATGGAGGAAATTGAATTGCTYTATCCAAACA 386 001AAGAATTTACAATGRAAGAAATTTGAATTGATTTATCCAAACCAAGTATTTGAAAAATGAAAGAAATTAAAATCAAAACAATTCAAATTTTAGACATTTTAAATTCTTTGAAATTTCTGATYCCAACACAAGATAAATGTTTTTCTCGTGCTTGATTG[C/T]GATGGTCATTTCCCACCGRTAAGGTTGGAATAACAATATTTGTTGAAATTTTAAGTCGCTTTAACTTAGAAATGTGGTTCTAGCAAGTGTTAATTTACCTTCCTTTGACAATTCATATAATATTTAAGATTGCTAATGAATGAGAAACAAAGTACTTTCGTTTTGCATTTTTTTTTCACAA GAAGTCAAAGAACCTTTTT S17156-GGTTATTTCTACTAAAGTTCTCGATCTAACGGCTTATTTAATT 390 001TTTTATTAGGAAAGGGAGGACAAATTCATTTCAAGAAAGCTATAATTTTATTTGTTGACCATCATTAAAAGAAAAGAAAAATTAAGGCATACTAAATTTACAATTTAATTAAGGAAAAACTCAAGAATGCCCTTCCAATGAAATAAAGCACTTGGAT[A/G]CCTGCAGGGTCAATTAGTTGTTGAAATCAGAARAACATTCTGAAAGCATCAACAACTTTCTCAGGCCTGTCAAAARTACAAAGGGTATATTCTTAAGAGGTTGAACAAATCATTTTACTATTCACTGAAATCCTATGTTAACTAAAGTTACTTACCAGTCCTCTTGTGGCATATGACC AGCTCCTTCTATCAATTTAAGCS17159- AAATTAGTGAAAKAAATCTTATTTTAAAGAAGGTAGATGTAT 394 001ATATGCGTACGTGTACCGACATTCACAAGCAATTAATTCAAATCAATAATTGAAATAACGTGGGGAAGTGCTCTTATGTTTTTTGAATAACATTGAAAAGAAACAGCGGCAATTTAAACTTYAAAGTCTCCAGCCYAACAAATCTCAAATGGGATCAT[A/G]GGTGGACCACGTGTCTTCCASAATATAGARTGTTGCTAGGTGCACCCARCATTCTTTAAAAATGAYAAAATTATCCCTGYYAATTTCTCCCCTTACCTTACGGATCAAATTGATCCGTAAAATACTTACGGATCAACTTGATCCGTAAGGDATATTTTTGTCTTTTCGTGGTTAGTGC TRGATGCACCAGCAATAATACTS08590-1 CTTTCATGTAAGAAGTCATTTGATATTAACAATGAAGTTATTT 399ATCTTCTCTTGACGCTGATGGACTACTTGTCTATTTCCAGCTATGAAGTTATTTATTAATTTGACTTCTCATTAACGCATTTTSTGTTCCTAATTRGTTTAGAACAACTAAAGACCCTTGAAAGACGACCAAAATTGTTTGTCTTGTGTTGCAGATC[A/G]GTTGTCATTTGGCCCGCGTGTACGGCTGCGGATAAGTTATTTATCGAAATAAGTGTCAGATCAAAGGACGATCTACGTCCCTTAAAAATTTCAATGACAACAAACACATTATAAGAATTTATTTATATTTTAAATTAAGCATCGCCTTTCATCCTAACAAATGTATTTTTAACGCAGATTAT TCGTCYATAACATTATTT S17242-GTATGAAAATGATTAGTGCTGTGACCTGTGGAMTTTTCCTAA 403 001CTAAATACATTTCTTTCACAATTGATGACGTTACAAAGAAAGTGAACTACAACTAATGCATATAATGTGTCTTTGTATGACCGTATCCAGGCATAACAAAACCATTTAAAGTTCAAGATACGCAATTACTTGGGGAATAAACATCGTGCTTTATAATT[A/C]TTGTTGTTATGTCACTACGTCAAGGCACTCTGCTATCACGCCATTGTATTTTAATTTATCGCAATAATCAGTCTTAAATGTTTTCGAAAATAAGATATTGTTTTATGATATAAATTTTTTGCACTAAAGTCGAATAATGTCTCTTTCTTTGTAAGCTTTCTTGTTATTGGGCACATGTATGCG TTTACAAGGAGAAAATG S17166-ATGCATATGTGTGTGTGTGTATAAATGGGTTTTTAAAAAATGT 408 001TGTCAACAAATAAAAAAAAGGTAATTTCATTGAATTTTATATTAAGCTAACAATTTATTGCTGCAATTTTTATTTTGGCTCGATCATATTAAGCTTAATTAAGTCCGCAAACTGTAGTACAAATCAATTTGGACCAACACATGTCCTCCACAAGACA[C/T]GCAGCAGAAGCCCATTTAATCAAATGACAAAAGGTAAATGCTAAATAAACTTYCCAAGTTACTTTCTACAACCCCCTTTTCGTTTTGATTTACCTTTATTCCAAACTYACCTTTTATCTTCTTCAACTCCCTTTATAGTTTTATTATATCABTCATGGGCACACTCCCTCTTCTCACAGTCGT ACCAGTCATATATGCAC S17167-GAAATTTTAACTAAATACATAAGACTTKTTTAGGGTGGTTATA 413 001AGTTTTTTATTTTTGGTTTTCACATGTAATTTTCAAAACAAAACATTRTTTGATAAAGATAGAGTTCAAATAATTTTTAATTTAATTTTAAAATACTTTTACATTCATTTTTTAAACTAAAAAAAAAGATCTTAAAATTTGATTTTTAGTTTTAAAA[A/G]AGCACAGTTACCCTACATTTGAAAATGACCCATTTTGTTATTGTTACCACTATTGTTGAYACCACCAACATCACTATCATTTTCACCATCACTGACACTACAACCATCACAACCAATATCACCATTATCATTGTCAATCACAACTATCATCACCACCCGCCATTAACATTGGCATCACTGTTGT TATTAYTGTCGTCATC S08539-1TGTTAAATYTATTTTTTTTAGTTAAATATATAAATACTCACTCT 418TATTYTTTTTCTTGTRTAACTNTTTTACNAATGTTATCTTTCACTTHTGTAAAGAGTCAACAAGARGTTATGCATATTTTTCATGAGAGATTAACATGYTTTRAGTATCATGCATYCAAGATCAWTGRTTGATCATCATTGTTAGAGCTTTGAAGA[A/G]TTCTTATTYTTTGGACTCAARGTGTATTCAATTCAATAATCCGTTCATTYAAGATTATTTTTAAATATATTTTGATGATCATAATACAATTACAAAACCAARACRCTAAAAAATAATTTATTTAAATAATAAAAAWAATTTATCCAAATGATTYCTAACATATATGTTGATGATCACAATACA ATTGTAACACAAGRTC S17178-ATCGCATTTAGTGTTCCTTTGCCATCGTTAATGAAGTTTTCCA 422 001GTAGTGYTGCTTATTCGTTTTCCTTTTTTGGGAAATTTTTKATAATATGTCCATWGAATCCTYAACACTTGCAAATTAGATAAAGGCCTCCATACTCAACATTGAATCTATGATTGTGAAACCAAACCTGTCCCACCACCATTCGGCTAAAGTCAAT[C/T]TTTATACACACCTTGACWAACTTTTTTTATGATGCATCCATGGTTGAAATATCAATTCTCAYGGGTCGTTGTTCTGCTGAAGCTAAAGCTACAAGAACACTTTCATCATAATACTCTAACTCTAAAAACGAGATCTTTATCCAAACTAAGGTATTGTTAACCTTCATATTCAATGGTTTGAA ATCCAACGACCGTAGTCT S17179-AGGGAATATGCATGATAACGAAGCAGGACTCGAKCATTTTCT 426 001TCTTCTTGGTCAACATATATATGGGGCCTAGCTAATTAACTTCTTAAATTAATTAGATTATGTCTACAAATTTATTTCAATTGTAKATTTAWATTAAAAAATCATTTTTSAATCAAGTTCAAATTAAAAAATATTTTCTAACTCTAAAAGCAAACTGG[A/G]ACATAATTTGGGCACCTAACTAAGTAAACTGGGTTAGTGAGGTTTATCTCAYCGATGTGGGYGTATTTTTTTGYAATAAGTTTCATTTTTGGCTTATTKTTCAATAATATAGAAAAAAATGTGATACGATAAATTATTTTTGGTAATATTTAACCCAACTTTTTTNGTTTTTGTTTTTTTT CCTTAAACACTCTTTATGTS17180- TATACAGATACTACTCATTTTTAACTTTAATTAGAAATAGTAT 430 001CAAAACCACGTATTAAACTGTATCCAAGTTTATCTTTTAAGAAATTATTCGTTTTTATTTGGTTTGTTAACTAGTACTATTAATTTTGTTCAGTGCATTTCCCATAGAAAGTTATTTGTTCTTTCTATTTTGAATTTGATTGCAAGATATTCAACTT[A/C]ACTGAAAGCTTACTAGGTTTTATCATTTCTTCTAGTTTTATTATACAAATCTTTATAATACTTTTTRCAAKTTTTTTTTTTCTCATTTTATCCTATCTTGTCTCAGATTTTTTTCTTATTTTTCTCACATTGTAAKAATTGTAAAAAAAGAAAGGCGTACTTTACTCAGCGCAAAKAAATTAATCATT AATTCATTATAG S17181-TATTATTAGGCTTTTCACATTTAAGGACTGGTAAAAATRTGAC 434 001TAGTTGACTGATATTAGTGTATTGTTATTTCTTATCTAATTTTTTATATGYAATTTTGAAATTTATATTGATACACTCACATATATCCCAKCATATCGATTATTGATATACCGTATCACTATTTATAKGTAATCACTAAAATTACACACTTAAATTA[C/G]CACTAACTTTAGRGCACATTATTTTCTGGAAAGATGTAATACAAAATTGGCCCATTAGCTCTTTTGAGTTTTGACCCTAAACCTTAAACACATTCCGTTTCTGTATAGTCTGTGGTCTATGATTTTGATGTKTTCATTTGTTTTATGTGCAACTAATATTAAACAAAAACACTTGAAAATCGA TAAGCACAGAAGGTATC S17182-AAAATTAATTGGTGAACCATATATCATCTCTAGAAATTATATT 438 001TAGAAAGACCAAACTCATCCTCATGCTCCTGAAGAAGAACAGAAAGAGCTTTGGTTATCTCTTCTGCTGCCGGAATAAACTAGGTTTGGAGCTCTACCATAGCTTTGGACTCAGATATACATAGATGAGAGGTGACAAGTGAAAACACCCTATTTTA[A/T]GAATATTCCATCAACATTTATGACCTATTACACTTACATATCTCTTTTTTCTCTCTTTCTCTAAGCMTTGGATAGCATGCATGCATGGAGTGGTCAATGCAACATTTTCCTATAATATTGTTACATCTTTATCTCAAACAACCTTTGTAGCAATGTTCCTATAAATAACCCCTGTCTCTTC AACTCTCACAGTGACTTTG S17183-AAAAACTTATAAGGTATTTTTATTATTTAAATGAKTAATACCA 442 001CCGACTTWGGCATAATTACATGACTAATTTTGCCGTTACTTGAAATGAAGACGAGAGAACTTATAGCGTGGAATCCGTGGGAGCACAATGTTTGTGGGGCATGGGAGATCTGGAGCCGTTCATTGACGATGTGGTTTGATCGTGCGGTGGATGTGAA[G/T]TGCCGACAGGTAATACAGGTAAATGGTGGCCACGHATGCATGTAAAAAAATGAATGAAGTTTATCTGTTTATACATTGAATGATGAAAATGGTGGTGGAGGAAGTCTTATTCTTCTTCGGTTGGTGGGTCCCMCTTAGATTTTGGTTGAGGTGRCACCATCTTTGAAAAGAGATTTC GGAAGATAGCTAGAATAAGTGAAS02780-1 GGCATGGAAGGGCTACATTTTCTGTTCTTCTTTTTCAGGTTCC 447TTTGTAACTTACCATCTATCTAGAAACTGCAGGATTCTCTTGTAAAATAAAATATTAAATGATATAATACTTGAGATATGTAGTTGGCTAAAYTTCATCTTATATGAGGCATTTGCTTCAATTTTCCAGACTATTGCCTTTACCTTCTAGACTCTGG[A/G]TAACCTGAACTGCATATCMTATAGGGGCAAAAGTATGTTATTTTGTCAGCATATAAACATGTTTGCATCCTATACAGTCAAGTATTCTACACAGATACTATAGAAAGTAGAAAGAATAGTGGTRCTTTTCACTTGTTTCTGTTGAAAACTGAATACAAAGATATAGAGAGAGTAGAGAGA AAAGGGAGATAAGGTTTCTC S12107-1GAGAAGGTGATAATAATAAATATGAAAATGACTTGAGATTYT 452GACTCTTGACTCCTAACCAAAATTTKAAAGCTTTTTTACACAGGGAGTTCCACTTTGAATTCCCCATCCTTGAAAGAAGTGGGGTTCACCMAATGCTACAGCACGAAACTTTTCCATCTTGGTGRCAAAGTGCGAACAATATTGAAGGTGACAATAGA[G/T]GGAGYCGATTGGGAAGGTGATATAAATTCTGCGCCCATGCAACAGTTTGAGGAGGAGGCAGCCTGAGTKAGTTTAATTTGGTGACAATTCCCCTCGACTTGTATGTAAGTACATACATTGATAATTATTTCTCATGGACATGCAATTAATATATGCTGATCAACTGCTACTAACTGA GNGAGAGAAGGCATTAAATATCTS03624-1 CTCTTGGTGCAAAAAAAWNTACACTATAGAAATCATGGTAGG 457TATGAMTTTTAAGGTAGTTATTGTACAGGCCAATAAACTTACCATCGATGTATAGACTATAGACKATTTTCTCTTTATATATGAGCTGTTTATCCATACTTTTTTTTCTCAAAAACATTACATGCATAACCTCTCATCATGTAATCATTTAATATGTG[A/G]CACTAATGATGCTAACTTGAGAGAAATTTACCTCTAATCTTATTTGCAGATGCATCTACTTCTTCATGCTCCACCGCAAGATCATCTGTTATTGTAGTGATTATTCTAATCTCAGGGCAATCATCTTTACAAGAAACATCAAGACTATCTGCTTCTTCTGGTCCTAACTGTTCATCCCGT TCAGAAGAATAATGAATTAAS01953-1 TTATTGAAAAATATAGACTTATTCCGAAAGTATATCTCCAAT 462WCTGTGAATCATAGTTCCAGAAATACATTTCTAGAATAGATATATGTAATTCTGGAAAGACATTTCCAAAAAGCAAAAGGAGTGTACTTCTTTATGAAAAACGGTGAAGGGTATGAGGGTGTDCTTAGGAAACTGGTGTAAATATCAAAATTCCTTCT[C/T]CACTTKATTGATTAAAAAAGAGGCACAAATCAAAGCAACAAAGGCTCCAAAATTAGTGGCCCGACACGATAGATAAAAGGGAATTGCTATATCCAGTTCCTCTTTTTGCTAATACACTCCCATTTTAATTTTTATTTTCAAAAGTACCCCTAATAAATACACTCCCTGTACCATGAC ATCATCATCATCCAACCTACGAGS00111-1 TTTGGCCCAATCCAATCCTCATAATCAACCTCTCTCTCTGACT 467GTTCACTCTGTGTTTGGAGGTGGAAACTTAGGGTATGATTTCTGATTCCCCTTCCTTCTCGCTCGTTCTCTGCTTTAATCCATCAACTATCCTTCTWACTCATATTTCTTCACTGATTCAAGATACGATCAAGTTTCCTTATCATTTGCTCCTAATT[A/G]CGTTTACCCTATACACACTTTTCCAGTTATTCACCRAAACCAACAAATAACAAATTTCAGGTTGTTGGAGAAATTGTTCTGTTGGGGGGATAYGATGTCGATGGAGAAGGAAGCTTCAAGCTCCACACCTACGCGCAAATTGTCGTGCACTGCATGCTTCGACGCTGTCTATTTCTGCTACTG TAATACCCATTGCCCTA S04180-1GATGATAAAACTTGGGGAGAATTTTGTCAAATCCTCCCCAGC 472GCATTTCTTAGTCCATGCTAGCAGATTTACTTTTTTTTTTTTCCATTTCTTCTGGTTGTGTAATTCAGGGATTAATYGATAATTAGACGACATGATTATGTAAATATATGTGCATTCACCATTTATGAATTTTGATCCTTATGTAGTCTTACATTGAC[A/G]CTGTTCCTTTCTCTWTATAATTGTGGCACATTATTCTGGGTTTTCATTTTTCAGTATTTGATTTCTCTCWACATCATGCACTGAGCACCTGCGTTAGGCTGAAAGAAAATAAATTAATAATGTTTTGATTCATAAMCTACAGAATTCAAGCTTTCCTTTAGTATYAACTTATTGAGTAGCTAA TGGCMAAATTGGAATTG S01008-1TATGTCAMCTTCACCTTGGGCAGRAAAGAAATTCCGTACTTG 477GACTTAAAGAATTTTCATGTTAAGCTATAACAATCAGAGAAAGATATTAATGAAGCAGCAAGCACATAATATGGAGATATGTGAGTTGCACCTTCAATCTTGGAGGACAAATCATGCACTGGATTGTGAAGAGAATATAAGCATATAGACTTACAGWG[C/G]AATTGTTACAYGTAGCAAAACTACATGAATAACAATCTAGTTAAAGCAAGGGATGCATACTAACAAACATCAAACTCTTATCACCTCATCTAGTCCCACGGTGGATCTAGTTTGAAACATGTAAGCAGTCTTAAAGCAAAATAGCAGGCATATSGTATCTATCTCAAACAGAAGT GGATAKAACAGTAAACCACATGCCAS12862-1 GGGACCTAATTTGAAACATTCAAGTAAAATATATTGTTTAATC 482TACCTATTACATCAAGGTGATGACCTTTTTAACCTAACCTACTACTCACATCCTCACCAATATTCAAGGATTGAGTCATTATGACWTATCAATATGATACACGATTGCACCCATATCGACCTTATTGTGTGTTCCATACTCTGAATATGATCGAATC[C/T]GATAAATGTTCATCGAAACAACCGGATMAATTACAGCTTGAGGATACACAACCCTCGAACCTTAAGTATAATGTACGTAAAGGCTAAGGCTTGAGGATCGGGTTASAATCCGAGATGTAATTCATTTTCGTTTTAGTTCATGTTGACTGATACACATGTCATCCTGCACTTGTCACATG GGGTGTCCTACGTGGTTTACTS12867-1 ATTGTAATATAATTGAAANAAAACATGCATTCATGATATGTA 487TTACCGGCATTCCAACCATGGCGCGCGGATGATGAAAAATGGTTGTAACTTCAATCAGACTTGTATTCACAATTAAGCAAAACTGAAACCCAAACACACGTTAAAACTCTTGTTCAGCTCGAGCTTATARCATTAMGAGATCATGACCACATGTAACT[A/G]TTATTATAACACACACATACACACATGAGAAGGGATCATATTTATTCTAGGATCAAATATACATGTGTGGGACCACTTGAACACAAAGTTATGTAGARTAGTTGTTTCATGCCATTGCTAATCAGGACTTCTCACTGCCAATCTATGTGTCTCATTCTCTCTAATMTCTCTGTCATTTT GTGTCTCATTCACTAGGATGAS04966-1 CTCATCACAGCATGCTTATGGCGTTGTCACACWAAAGCATTG 492AAGATAGATGCAGATAAGGATGTTCGAATGATGGTCGCCGTCAACGCACGTGCTAAGTTCAATCCTCCTTTACCTGTTGGTTATTACGGTAATGCCATTGCATACCCAGCAGCAGTCACCACAGCAGGGAAGCTTTGTGGAAATCCATTTGGGTATGC[A/T]GTGGAATTAATAAATAAAGTGAAAGGTAAGGCCACACAAGAGTAWATGCATTCTGTGGCAGATCTATTGGCTATTAAGGGACGATACATACCAAGAATGGTGAGGTCTCTTACTGTGTCAGATTTGAGAGGTTTTGATCCCAGACAAATTGATTTTGGGTGGGGCCATGCTCTCTAT GCTGGACCAGCTCAAGGAGGCCTS10631-1 AACCGTTATGGTTGGGGATCGTTGCTACCAAAACCAAAATCT 497CGGGACGGATCAATGTCCCAATGCTTGGTATGTCTGATGCCACTTTTTGATTCTATGTCTCCTCAATTTTTTTTTTCTGATTCCGTCTATGATTGYTAGATTAGATCAAAAGAATTAGCCGGTTTACTTGGAATGTTTGAATCATTTCTAATAAGATC[C/T]GAGTTGGAAGAAAAGACACATGTCTAGAAATTCGACAGATCTTGCATCAAATAGAAGGGAAAATAATTAATCATTTTCATAATTTTTTTTAGTATTTACGTCCTAATTAGTAGTCAATATGATAATTCTACCAATGAGGTTTATAGGTCATGTAAGTAACTGTTTATTATTCAGAAAAATA GGAATACRTAACATAAAAT S0174-1ATCATAATTATTGCAAAAACAATATCTGGTCTAGTGTGGGCT 502AGATAAATAAGTTTTCCCTATCRGTCTTTGATATCAAGCCTATTTGAGCTCTCCCATTCCTATCCAATGATTTTGCTTGATGAGCTCTCCATATGTTTTACGACCCAATTTGCTTGTCTCTCTAAGAAGATMAATGGCATATTTTCTTTGAGAGATAA[A/C]GATGCCTTTTTTGGAGCAGGCAACTTCTATTTTCAGGATTTTTTTCAGCTTTCCTAGTTGCTTCATTTCAAATTGAGTTGTCAACCTTTCCCTTAGGATTTGTTTTCAACTTCATCATTTCCTGCAACAAACATATCATCTACTTAGACCAAAAGGATTGCCAATTTACCTGTCTGAAAAT GCTTTATAGAGTGTGGTCA S16594-CAGAGGTTGAATGGAGAATTTGCACCATTTGGGAAGCTGCTT 507 001ATGGCCTGATTCCTACAAGTTCCTCAGCTGTTGATCTTCCGGAAATTATAGTTGCAACCCCACTACAGCCTCCCGTGCTGTCATGGAATTTGTACATACCCCTATTGAAGGTCCTGGAATATCTTCCTCGTGGAAGCCCATCAGAGGCATGTCTTATG[A/T]AAATATTTGCTGCTACAGTGGAAGCTATTCTTCAGAGGACATTTCCACCTGAGTCCACTAGAGAACAAAACAGAAAATCAAAATACCTAGCTGGCATAGGCTTTGGCTCTGCCTCAAAAAACCTGGCCGTGGCAGAACTTCGTACAATGGTTCATTCACTCTTCTTAGAATCATGTGC ATCTGTAGAGCTTGCTTCACGCS02777-1 CTTTGAAAATATAAAGTAAAATATTTTTATGTGAATCTATATA 512TATAAAATCTAATATCACATTCACACCCKAAAATTTATCTCATGCGAACATGCTTACAAAAGCATTGAATTGGAAAMAAACATATCGAAGTGCAAATACGGTATATCATACTAAATATCAGTTATATTTCCTTAATTTTAAAAGTTTGTTATCTTCC[A/G]CTTTAGACTATATATTCATCATTTTCCAAAATTTCAGTTTCCATTTCAAGTCGAGTTTGATTCAATTCAGCTGTTTAGCGATDTTGAAGTGGAAACAGTCAGTAGATTTAGTGTACTGATGAGGTTGAACACAAGTTAGGATATTACTGTCTTGCATGTGAATTTGTTGGTCAATTACA CTTGCTTCCATTCACWAAATT

The SNP markers identified in these studies could be useful, forexample, for detecting and/or selecting soybean plants with a preferredreproductive growth phenotype. The physical position of each SNP isprovided in Table 24 based upon the JGI Glyma1 assembly (Schmutz et al.(2010) Nature 463:178-183). Any marker capable of detecting apolymorphism at one of these physical positions, or a marker associated,linked, or closely linked thereto, could also be useful, for example,for detecting and/or selecting soybean plants with an alteredreproductive growth phenotype. In some examples, the SNP allele presentin the first parental line could be used as a favorable allele to detector select plants with altered time to R1, such as a shorter time tofloral initiation. In other examples, the SNP allele present in thesecond parent line could be used as an allele to detect or select plantsfor unaltered time to R1.

These SNP markers could also be used to determine a preferred ornon-preferred haplotype. In certain examples, a favorable haplotypewould include any combinations of two or more of the alleles provided inTables 24 and 25. In addition to the markers listed in the tables (e.g.,Tables 26-27), other closely linked markers could also be useful fordetecting and/or selecting soybean plants with a preferred reproductivegrowth phenotype, for example exemplary markers provided in Tables28-46. Further, chromosome intervals containing the markers providedherein could also be used.

TABLE 28 Locus LG (ch) Physical Genetic (cM) BARC-048987-10780 A1_(5)266,909 0.00 BARC-040651-07808 A1_(5) 620,344 2.45 BARC-053261-11776A1_(5) 937,369 3.45 BARCSOYSSR_05_0046 A1_(5) 995,905 3.63 Sat_137A1_(5) 995,905 3.63 BARC-023449-05395 A1_(5) 1,050,663 4.06BARC-023411-05376 A1_(5) 1,051,044 4.07 BARC-023409-05375 A1_(5)1,075,339 11.17 BARC-014287-01306 A1_(5) 2,558,104 14.78BARCSOYSSR_05_0149 A1_(5) 2,887,437 16.35 Sat_368 A1_(5) 2,887,437 16.35BARC-019415-03923 A1_(5) 3,021,580 17.65 BARCSOYSSR_05_0179 A1_(5)3,442,467 18.91 Satt276 A1_(5) 3,442,467 18.91 BARC-010741-00738 A1_(5)3,507,636 19.30 BARC-021573-04148 A1_(5) 3,645,205 20.28BARC-014883-01912 A1_(5) 4,043,928 24.07 BARC-065065-19078 A1_(5)4,359,496 24.96 BARC-058785-15434 A1_(5) 6,852,194 27.64BARCSOYSSR_05_0427 A1_(5) 11,000,000 28.30 Satt248 A1_(5) 11,000,00028.30 BARC-024893-10355 A1_(5) 20,004,473 28.39 BARCSOYSSR_05_0581A1_(5) 23,929,087 28.82 Satt364 A1_(5) 23,929,087 28.82BARC-063687-18439 A1_(5) 26,716,236 30.63 BARC-050075-09365 A1_(5)27,637,336 31.37 BARC-024801-10347 A1_(5) 28,414,533 32.10BARC-048025-10453 A1_(5) 28,878,538 32.40 BARC-065675-19641 A1_(5)29,021,677 32.61 BARC-010403-00623 A1_(5) 29,178,219 32.62BARC-050757-09856 A1_(5) 29,489,647 32.90 BARC-058161-15150 A1_(5)30,394,323 33.43 S01435-1 A1_(5) 30,568,085 33.61 BARC-064245-18594A1_(5) 30,754,815 33.81 BARC-017329-02265 A1_(5) 31,297,779 34.18BARC-054977-12201 A1_(5) 31,506,542 35.05 BARC-040459-07745 A1_(5)31,674,074 36.10 BARC-050067-09358 A1_(5) 31,676,019 36.10BARC-056463-14388 A1_(5) 31,773,037 37.40 BARC-052343-11430 A1_(5)31,884,662 37.90 BARC-024619-05489 A1_(5) 31,891,048 37.90BARC-020479-04637 A1_(5) 32,055,300 38.96 BARC-053443-11853 A1_(5)32,393,030 41.63 BARC-044557-08720 A1_(5) 32,913,357 44.01BARC-025997-05216 A1_(5) 33,489,849 46.79 BARC-031361-07059 A1_(5)33,680,124 47.27 BARC-049091-10809 A1_(5) 33,699,369 47.27BARCSOYSSR_05_0991 A1_(5) 33,718,230 47.78 Sat_407 A1_(5) 33,718,23047.78 BARC-042853-08438 A1_(5) 34,115,224 49.47 BARCSOYSSR_05_1021A1_(5) 34,158,338 50.27 Satt648 A1_(5) 34,158,338 50.27BARC-031031-06987 A1_(5) 34,294,398 50.98 BARC-018011-02495 A1_(5)34,294,844 50.98 BARC-030907-06967 A1_(5) 34,436,914 51.76BARC-020229-04499 A1_(5) 34,514,905 52.37 BARC-020401-04601 A1_(5)34,610,781 52.77 BARC-026129-05274 A1_(5) 34,684,784 53.01BARC-037207-06739 A1_(5) 35,104,770 53.77 BARC-047054-12831 A1_(5)35,261,608 54.34 BARC-049797-09148 A1_(5) 35,313,037 54.53BARC-038407-10072 A1_(5) 35,428,921 56.14 BARC-039495-07502 A1_(5)35,690,504 57.95 BARCSOYSSR_05_1115 A1_(5) 35,700,565 59.24 Satt619A1_(5) 35,700,565 59.24 BARC-052589-11517 A1_(5) 35,898,964 61.04BARC-031957-07230 A1_(5) 35,965,810 61.92 BARCSOYSSR_05_1134 A1_(5)36,180,326 62.70 Satt545 A1_(5) 36,180,326 62.70 BARC-051453-11119A1_(5) 36,454,309 63.49

TABLE 29 Locus LG (ch) Physical Genetic (cM) BARC-021937-04237 A2_(8)1,466,024 9.57 BARC-039839-07593 A2_(8) 2,035,742 11.55BARC-014435-01365 A2_(8) 2,246,693 12.86 BARC-021463-04108 A2_(8)2,986,176 14.66 BARC-031701-07215 A2_(8) 3,056,358 15.45BARC-044051-08595 A2_(8) 3,174,985 16.44 BARC-032579-08998 A2_(8)3,307,480 16.96 BARC-016965-02168 A2_(8) 3,341,884 20.27BARC-065591-19578 A2_(8) 3,533,588 21.02 BARC-028679-05986 A2_(8)3,800,144 22.79 BARCSOYSSR_08_0206 A2_(8) 4,000,361 23.82 Satt207 A2_(8)4,000,361 23.82 BARC-013537-01155 A2_(8) 4,316,426 25.69BARCSOYSSR_08_0262 A2_(8) 5,027,347 30.18 Satt493 A2_(8) 5,027,347 30.18BARCSOYSSR_08_0273 A2_(8) 5,176,019 30.52 Satt589 A2_(8) 5,176,019 30.52BARC-025925-05158 A2_(8) 5,278,616 31.20 BARCSOYSSR_08_0305 A2_(8)5,715,429 32.94 Sat_409 A2_(8) 5,715,429 32.94 BARC-039593-07509 A2_(8)5,765,344 33.26 BARCSOYSSR_08_0371 A2_(8) 6,751,708 38.87 Satt315 A2_(8)6,751,708 38.87 BARC-025811-05087 A2_(8) 7,464,186 40.48 S01239-1 A2_(8)7,464,336 40.49 BARC-028361-05840 A2_(8) 7,716,559 44.48BARC-021329-04038 A2_(8) 7,824,774 45.22 BARC-062265-17733 A2_(8)7,963,465 45.59 BARC-028309-05824 A2_(8) 8,082,742 45.61BARC-045047-08867 A2_(8) 8,110,728 45.62 BARCSOYSSR_08_0454 A2_(8)8,219,326 46.28 Satt632 A2_(8) 8,219,326 46.28 BARC-012525-00285 A2_(8)8,279,099 46.44 BARCSOYSSR_08_0458 A2_(8) 8,279,445 46.56 Sat_162 A2_(8)8,279,445 46.56 BARC-048453-10596 A2_(8) 8,368,060 47.08BARC-038291-07245 A2_(8) 8,380,220 47.08 BARC-039247-07486 A2_(8)8,469,553 47.11 BARC-014511-01568 A2_(8) 8,887,107 47.38BARC-027690-06633 A2_(8) 8,943,498 47.56 BARCSOYSSR_08_0506 A2_(8)9,211,913 47.87 Sat_215 A2_(8) 9,211,913 47.87 BARC-059853-16139 A2_(8)9,407,115 48.04 BARC-027618-06622 A2_(8) 9,578,780 48.49BARC-026091-05255 A2_(8) 9,749,954 50.42 BARC-043119-08535 A2_(8)9,997,689 51.31 BARC-039145-07456 A2_(8) 10,166,248 51.92BARC-038631-07266 A2_(8) 10,303,015 52.38 BARCSOYSSR_08_0579 A2_(8)10,721,802 53.55 Satt424 A2_(8) 10,721,802 53.55 BARC-030611-06911A2_(8) 10,826,342 55.06 BARC-020307-04548 A2_(8) 10,947,663 55.10BARC-045081-08872 A2_(8) 10,954,474 55.11 BARC-029671-06303 A2_(8)11,536,514 56.73 BARC-027614-06619 A2_(8) 11,570,109 56.88BARC-040893-07862 A2_(8) 11,845,155 57.43 BARC-044869-08827 A2_(8)11,922,404 58.86 BARC-018941-03041 A2_(8) 12,022,737 59.30BARC-014665-01618 A2_(8) 12,471,926 61.07 BARC-040357-07716 A2_(8)12,972,647 62.13 BARC-029593-06225 A2_(8) 13,111,220 63.06BARC-044663-08756 A2_(8) 13,446,458 64.42 BARC-041459-08002 A2_(8)13,463,703 64.42 BARC-029315-06150 A2_(8) 13,902,606 66.58BARC-055265-13154 A2_(8) 14,004,161 66.58 BARC-032791-09038 A2_(8)14,265,356 67.71 BARC-038455-10089 A2_(8) 14,850,506 69.58BARCSOYSSR_08_0849 A2_(8) 15,140,599 70.95 Sat_199 A2_(8) 15,140,59970.95 BARCSOYSSR_08_0879 A2_(8) 15,562,968 72.78 Sat_233 A2_(8)15,562,968 72.78 BARC-031627-07124 A2_(8) 15,733,404 75.01BARC-039899-07603 A2_(8) 15,818,113 76.43 S00780-1 A2_(8) 15,841,57076.47 BARC-029669-06297 A2_(8) 16,164,943 77.06 BARC-049031-10792 A2_(8)16,250,468 77.06 BARC-049045-10806 A2_(8) 16,250,599 77.06BARCSOYSSR_08_0909 A2_(8) 16,427,750 77.51 Satt377 A2_(8) 16,427,75077.51 BARC-042491-08277 A2_(8) 16,624,607 79.14 BARC-022387-04319 A2_(8)16,839,499 81.25 BARCSOYSSR_08_0948 A2_(8) 17,076,816 83.61 Satt525A2_(8) 17,076,816 83.61 BARC-031601-07118 A2_(8) 17,167,641 84.15BARC-022445-04327 A2_(8) 17,410,233 85.38 BARC-063091-18238 A2_(8)17,412,255 85.58 BARC-028207-05794 A2_(8) 17,695,309 87.11BARC-013001-00417 A2_(8) 17,738,311 88.06 BARC-054097-12336 A2_(8)17,940,930 88.16 BARC-038877-07374 A2_(8) 17,940,998 88.16BARC-054143-12351 A2_(8) 17,945,325 88.16 BARC-059821-16111 A2_(8)18,439,010 89.50 BARC-041231-07943 A2_(8) 18,856,442 90.76BARC-027788-06671 A2_(8) 18,952,545 90.84 BARC-050061-09354 A2_(8)20,229,386 92.31 BARC-020835-03959 A2_(8) 20,441,412 92.31BARC-021629-04158 A2_(8) 20,530,558 92.53 BARC-010797-00750 A2_(8)21,133,646 92.81 BARC-019299-03876 A2_(8) 21,896,189 94.21BARC-011001-00815 A2_(8) 21,896,207 94.37 BARC-065451-19476 A2_(8)22,590,975 94.72 BARCSOYSSR_08_1216 A2_(8) 22,995,965 97.59 Sat_232A2_(8) 22,995,965 97.59 BARCSOYSSR_08_1226 A2_(8) 23,213,226 100.07Satt158 A2_(8) 23,213,226 100.07 BARC-061573-17277 A2_(8) 23,456,372101.45 BARC-055297-13184 A2_(8) 23,691,540 101.47 BARC-051883-11286A2_(8) 24,848,454 101.52 BARC-049593-09076 A2_(8) 29,150,451 101.52BARC-049595-09077 A2_(8) 29,158,623 101.52 BARC-059127-15620 A2_(8)34,040,540 101.52 BARC-050571-09743 A2_(8) 34,793,726 101.52BARC-010965-00797 A2_(8) 35,156,936 101.52 BARC-019295-03875 A2_(8)35,156,963 101.52 BARC-058307-15218 A2_(8) 35,334,725 101.52BARC-060765-16857 A2_(8) 35,475,655 101.58 BARC-061979-17603 A2_(8)35,484,031 101.58 BARC-049905-09236 A2_(8) 36,079,891 101.92BARC-049903-09231 A2_(8) 36,240,677 101.92 BARC-061059-17022 A2_(8)36,596,871 102.46 BARC-059569-15920 A2_(8) 37,183,791 102.46BARC-053631-11924 A2_(8) 37,319,425 102.46 BARC-053637-11925 A2_(8)37,564,284 102.46 BARC-049851-09173 A2_(8) 38,097,310 102.94BARC-028775-06010 A2_(8) 38,238,572 103.30 BARC-020321-04554 A2_(8)38,332,877 103.34 BARC-050125-09401 A2_(8) 38,344,641 103.34BARC-030625-06913 A2_(8) 38,346,614 103.34 BARC-010341-00598 A2_(8)38,999,975 103.57 BARC-062129-17664 A2_(8) 39,451,763 103.87BARCSOYSSR_08_1502 A2_(8) 39,470,511 104.54 Sat_097 A2_(8) 39,470,511104.54 BARC-017137-02222 A2_(8) 39,754,026 105.48 BARC-043095-08525A2_(8) 39,960,478 105.79

TABLE 30 Locus LG (ch) Physical Genetic (cM) BARC-017811-02392 B1_(11)29,924 5.55 BARC-058339-15238 B1_(11) 559,320 4.58 BARC-062833-18109B1_(11) 560,024 4.58 BARC-017915-02450 B1_(11) 1,481,336 2.82BARC-018583-02981 B1_(11) 1,656,830 2.54 BARCSOYSSR_11_0142 B1_(11)2,710,565 18.03 Sat_272 B1_(11) 2,710,565 18.03 BARC-041095-07905B1_(11) 3,684,393 23.86 BARCSOYSSR_11_0227 B1_(11) 4,224,531 25.64Sat_270 B1_(11) 4,224,531 25.64 BARC-014611-01591 B1_(11) 4,250,96526.17 S06925-1 B1_(11) 4,674,824 28.92 BARC-018713-03241 B1_(11)5,089,529 31.61 BARC-042439-08267 B1_(11) 5,123,196 31.81 S09951-1B1_(11) 5,231,500 32.04 BARC-018099-02516 B1_(11) 5,270,796 32.12BARC-032437-08975 B1_(11) 5,287,056 32.13 BARC-032333-08951 B1_(11)5,287,077 32.13 BARC-042989-08491 B1_(11) 5,938,208 37.81BARC-017097-02199 B1_(11) 6,020,848 37.95 BARC-900941-00964 B1_(11)6,166,382 38.32 BARC-016137-02291 B1_(11) 6,174,078 38.37BARCSOYSSR_11_0380 B1_(11) 6,961,225 40.95 Satt638 B1_(11) 6,961,22540.95 BARC-040851-07854 B1_(11) 7,619,584 44.65 BARC-044037-08588B1_(11) 7,688,341 45.33 S00170-1 B1_(11) 7,847,341 45.37BARC-025873-05130 B1_(11) 7,847,370 45.37 BARC-061085-17035 B1_(11)7,952,601 45.43 BARC-038623-10188 B1_(11) 7,996,138 45.45BARC-031547-07108 B1_(11) 8,492,168 46.25 BARC-050091-09377 B1_(11)8,582,563 46.56 BARCSOYSSR_11_0482 B1_(11) 8,879,510 49.07 Satt197B1_(11) 8,879,510 49.07 BARCSOYSSR_11_0496 B1_(11) 9,078,586 52.06Sat_247 B1_(11) 9,078,586 52.06 BARC-032817-09052 B1_(11) 10,319,33855.57 BARC-016279-02316 B1_(11) 10,804,852 61.61 BARC-022123-04287B1_(11) 11,269,342 63.49 BARC-050929-13806 B1_(11) 11,532,769 65.62BARC-054421-12081 B1_(11) 12,295,534 66.70 BARC-061409-17191 B1_(11)15,208,402 68.33 BARC-053713-11954 B1_(11) 15,545,136 69.17BARC-040309-07711 B1_(11) 15,576,761 69.17 BARCSOYSSR_11_0828 B1_(11)16,893,706 72.09 Sat_348 B1_(11) 16,893,706 72.09 BARCSOYSSR_11_0839B1_(11) 17,065,539 74.21 Satt597 B1_(11) 17,065,539 74.21BARC-059803-16097 B1_(11) 17,822,677 76.86 BARC-050205-09457 B1_(11)17,822,703 76.86

TABLE 31 Locus LG (ch) Physical Genetic (cM) BARCSOYSSR_14_0440 B2_(14)7,818,064 43.15 Sct_034 B2_(14) 7,818,064 43.15 BARC-064873-18956B2_(14) 8,340,001 45.46 BARCSOYSSR_14_0485 B2_(14) 8,642,764 45.66Satt416 B2_(14) 8,642,764 45.66 BARC-030967-06981 B2_(14) 8,902,64750.05 BARC-055677-13598 B2_(14) 9,318,033 53.92 BARC-014309-01312B2_(14) 9,642,001 54.51 BARC-052759-11611 B2_(14) 10,018,294 55.50BARC-052757-11610 B2_(14) 10,149,510 55.50 BARC-057817-14938 B2_(14)10,667,555 55.79 BARC-054615-12115 B2_(14) 10,699,554 56.10BARC-059553-15907 B2_(14) 10,708,292 56.10 BARC-051601-1175 B2_(14)11,283,799 56.33 BARC-051599-1174 B2_(14) 11,320,165 56.36BARC-065009-19043 B2_(14) 12,765,699 56.60 BARCSOYSSR_14_0663 B2_(14)13,784,029 56.81 Sat_355 B2_(14) 13,784,029 56.81 BARC-023673-03446B2_(14) 24,138,675 60.07 BARC-059375-15776 B2_(14) 30,148,286 63.48BARC-055413-13266 B2_(14) 30,458,374 63.48 BARC-062781-18055 B2_(14)30,561,889 63.48 BARC-057785-14922 B2_(14) 31,475,698 63.48BARC-049743-09137 B2_(14) 31,642,640 63.48 BARC-032443-08976 B2_(14)32,380,594 63.48 BARC-056587-14511 B2_(14) 33,084,741 63.48BARC-013927-01275 B2_(14) 33,571,308 63.48 BARC-062037-17640 B2_(14)33,950,948 63.48 BARC-018353-03589 B2_(14) 34,025,136 63.48BARC-031293-07038 B2_(14) 34,323,246 63.48 BARC-030997-06983 B2_(14)34,323,315 63.48 BARC-060347-16622 B2_(14) 34,621,804 63.48BARC-058131-15103 B2_(14) 34,818,582 63.48 BARC-057297-14680 B2_(14)34,821,875 63.48 BARC-061113-17055 B2_(14) 34,824,183 63.48BARC-058987-15541 B2_(14) 36,145,603 63.48 BARC-057997-15049 B2_(14)37,295,178 63.48 BARC-061279-17151 B2_(14) 37,903,944 63.48BARC-047146-12873 B2_(14) 38,163,669 63.48 BARC-060943-16979 B2_(14)38,284,031 63.48 BARC-062887-18145 B2_(14) 40,552,074 63.48BARC-023661-03445 B2_(14) 41,640,536 63.49 BARC-061125-17061 B2_(14)42,276,845 63.49 BARC-055593-13466 B2_(14) 42,735,542 63.71BARC-049657-09098 B2_(14) 43,839,403 64.21 BARC-901431-00997 B2_(14)43,846,938 64.21 BARC-052791-11622 B2_(14) 44,146,158 64.68BARC-052789-11619 B2_(14) 44,293,219 65.17 BARC-063857-18474 B2_(14)45,913,358 73.94 S04059-1 B2_(14) 46,138,053 75.42 BARC-038467-10112B2_(14) 46,213,791 75.91 BARCSOYSSR_14_1341 B2_(14) 46,246,865 78.09AW620774 B2_(14) 46,246,865 78.09 BARC-065655-19613 B2_(14) 46,710,43380.24 BARC-013273-00464 B2_(14) 46,714,178 80.36 BARC-016831-02340B2_(14) 46,885,648 81.19 S07851-1 B2_(14) 47,331,319 83.76BARCSOYSSR_14_1421 B2_(14) 47,849,686 86.76 Satt560 B2_(14) 47,849,68686.76 BARC-053447-11854 B2_(14) 48,055,573 86.97 BARC-024363-04860B2_(14) 48,668,529 93.81 BARC-024363-04857 B2_(14) 48,668,529 95.86BARC-059251-15691 B2_(14) 48,884,075 96.44 BARC-017211-02251 B2_(14)48,940,822 96.45 BARC-030849-06952 B2_(14) 49,276,286 96.76BARC-013859-01259 B2_(14) 49,292,092 96.86 BARC-041333-07967 B2_(14)49,362,025 96.89 BARC-030661-06918 B2_(14) 49,487,183 97.61BARC-017589-02630 B2_(14) 49,705,320 97.92

TABLE 32 Locus LG (ch) Physical Genetic (cM) BARCSOYSSR_04_0025 C1_(4)433,582 0.00 Sct_186 C1_(4) 433,582 0.00 BARCSOYSSR_04_0026 C1_(4)447,227 2.11 Satt690 C1_(4) 447,227 2.11 BARCSOYSSR_04_0035 C1_(4)525,154 2.97 SOYGPATR C1_(4) 525,154 2.97 BARC-030305-06851 C1_(4)963,864 5.03 BARC-044617-08741 C1_(4) 982,287 5.58 BARC-018919-03036C1_(4) 1,089,217 6.17 BARC-031853-07222 C1_(4) 1,163,728 6.77BARC-057913-15004 C1_(4) 1,250,289 10.04 BARC-014277-01301 C1_(4)1,431,400 10.61 BARC-016959-02166 C1_(4) 1,710,562 11.51BARC-030765-06943 C1_(4) 1,891,388 11.97 BARC-054289-12451 C1_(4)2,069,710 12.19 BARC-029425-06191 C1_(4) 2,207,639 12.33BARCSOYSSR_04_0125 C1_(4) 2,402,268 13.37 Satt194 C1_(4) 2,402,268 13.37BARC-039239-07481 C1_(4) 2,507,250 14.03 BARC-016519-02081 C1_(4)2,843,396 15.58 BARC-015981-02030 C1_(4) 3,205,314 16.51BARC-022353-04316 C1_(4) 3,348,266 16.72 BARC-031733-07217 C1_(4)4,054,929 19.50 BARC-044709-08764 C1_(4) 4,120,312 20.56BARCSOYSSR_04_0228 C1_(4) 4,172,835 20.97 Sat_337 C1_(4) 4,172,835 20.97BARC-020447-04622 C1_(4) 5,392,117 27.44 BARC-014361-01331 C1_(4)5,468,471 27.65 BARC-022437-04324 C1_(4) 5,468,475 27.71 S11659-1 C1_(4)5,754,268 29.24 BARC-044691-08761 C1_(4) 6,322,293 32.27BARC-044521-08714 C1_(4) 6,378,204 33.11 BARC-040777-07848 C1_(4)6,428,283 34.00 BARC-025825-05102 C1_(4) 6,684,059 36.48BARCSOYSSR_04_0416 C1_(4) 7,819,458 40.86 Satt578 C1_(4) 7,819,458 40.86BARC-041405-07979 C1_(4) 7,882,994 41.75 BARC-038309-10010 C1_(4)8,030,160 42.42 BARCSOYSSR_04_0430 C1_(4) 8,093,779 43.17 Satt607 C1_(4)8,093,779 43.17 BARC-062641-17963 C1_(4) 8,154,438 44.48BARC-017023-02178 C1_(4) 8,224,268 45.67 S04279-1 C1_(4) 8,295,779 45.75BARC-029943-06758 C1_(4) 8,465,328 45.96 BARCSOYSSR_04_0460 C1_(4)8,830,940 46.01 Satt646 C1_(4) 8,830,940 46.01 BARC-015923-02016 C1_(4)8,915,160 46.45 BARC-046068-10219 C1_(4) 9,120,496 47.07BARC-064923-19002 C1_(4) 9,168,034 47.07 BARC-063455-18377 C1_(4)9,170,865 47.07 BARC-053223-11766 C1_(4) 9,236,857 48.48BARC-053219-11764 C1_(4) 9,300,071 48.87 BARC-058645-15349 C1_(4)9,789,291 50.76 BARCSOYSSR_04_0579 C1_(4) 12,529,635 50.97 Sat_404C1_(4) 12,529,635 50.97 BARC-055359-13232 C1_(4) 14,079,084 51.08BARC-007901-00205 C1_(4) 14,985,510 51.13 BARC-060187-16464 C1_(4)16,789,799 51.74 BARC-020889-03981 C1_(4) 18,904,768 51.75BARC-057291-14674 C1_(4) 19,337,323 52.35 BARC-063099-18239 C1_(4)26,870,515 52.49 BARCSOYSSR_04_0881 C1_(4) 33,321,553 52.71 Satt399C1_(4) 33,321,553 52.71 BARC-063667-18427 C1_(4) 34,928,793 52.72BARC-058775-15427 C1_(4) 35,970,986 52.72 BARC-060917-16967 C1_(4)36,250,476 52.72 BARC-061273-17145 C1_(4) 36,403,199 52.72BARCSOYSSR_04_0953 C1_(4) 37,475,216 53.17 Sat_416 C1_(4) 37,475,21653.17 BARC-063499-18381 C1_(4) 38,018,967 53.30 BARC-059291-15718 C1_(4)38,496,133 53.84 BARC-059947-16237 C1_(4) 38,929,141 53.84 S02211-1C1_(4) 39,691,731 54.48 BARC-061329-17168 C1_(4) 40,179,629 54.89BARC-061983-17604 C1_(4) 40,650,236 55.78 BARCSOYSSR_04_1062 C1_(4)40,871,939 56.46 Satt476 C1_(4) 40,871,939 56.46 BARCSOYSSR_04_1072C1_(4) 41,223,589 58.35 Sat_042 C1_(4) 41,223,589 58.35BARC-020509-04645 C1_(4) 41,667,200 59.31 BARC-038989-07419 C1_(4)41,667,225 59.34 BARC-056153-14127 C1_(4) 41,872,671 60.01BARCSOYSSR_04_1140 C1_(4) 42,571,776 63.13 Satt670 C1_(4) 42,571,77663.13 BARCSOYSSR_04_1172 C1_(4) 43,039,754 66.04 Sat_311 C1_(4)43,039,754 66.04 BARC-030647-06914 C1_(4) 43,097,230 66.35BARC-042189-08197 C1_(4) 43,684,210 68.85 BARC-040387-07722 C1_(4)44,012,162 75.21 S08942-1 C1_(4) 44,725,098 80.59 BARC-044373-08692C1_(4) 44,746,648 80.76 BARC-052267-11398 C1_(4) 45,015,005 82.17BARC-022447-04328 C1_(4) 46,306,130 96.50 BARC-019093-03301 C1_(4)46,484,136 96.83 BARC-013699-01240 C1_(4) 46,578,102 97.43BARC-024187-04790 C1_(4) 46,813,397 100.53 BARC-015121-02570 C1_(4)46,896,236 100.57 BARCSOYSSR_04_1362 C1_(4) 46,964,916 101.22 Satt338C1_(4) 46,964,916 101.22 BARC-044427-08705 C1_(4) 47,116,996 102.47BARCSOYSSR_04_1382 C1_(4) 47,335,984 104.01 Satt682 C1_(4) 47,335,984104.01 BARC-061009-17004 C1_(4) 47,396,872 104.61 BARC-018629-03208C1_(4) 47,621,366 105.84 BARC-028671-05985 C1_(4) 48,121,255 108.24BARC-062835-18113 C1_(4) 48,196,149 108.93 BARC-032045-07244 C1_(4)48,918,109 110.22 BARC-041047-07901 C1_(4) 48,959,049 110.26BARC-029125-06087 C1_(4) 49,173,958 112.20

TABLE 33 Locus LG (ch) Physical Genetic (cM) S05742-1 C2_(6) 410,4424.88 BARCSOYSSR_06_0028 C2_(6) 488,872 4.98 Satt681 C2_(6) 488,872 4.98BARC-053027-11697 C2_(6) 651,027 5.19 BARC-015973-02029 C2_(6) 825,7986.11 BARC-035239-07157 C2_(6) 1,655,968 11.62 BARCSOYSSR_06_0107 C2_(6)1,839,799 12.98 Sat_130 C2_(6) 1,839,799 12.98 BARC-056069-14029 C2_(6)2,100,582 16.39 BARC-064413-18929 C2_(6) 3,130,074 23.21BARC-024137-04780 C2_(6) 3,370,117 23.66 BARC-042045-08161 C2_(6)3,427,039 23.81 BARC-016957-02165 C2_(6) 3,790,397 26.08BARCSOYSSR_06_0268 C2_(6) 4,677,084 29.63 Satt640 C2_(6) 4,677,084 29.63BARCSOYSSR_06_0283 C2_(6) 4,947,481 31.78 Sat_062 C2_(6) 4,947,481 31.78BARC-024049-04718 C2_(6) 5,375,750 33.01 BARC-027846-06691 C2_(6)5,400,643 33.29 BARC-013887-01262 C2_(6) 5,400,860 33.29BARC-014949-01931 C2_(6) 5,404,840 33.29 BARC-059985-16274 C2_(6)5,443,313 34.40 BARC-022163-04290 C2_(6) 5,492,796 34.43BARC-059997-16280 C2_(6) 5,498,347 35.37 BARC-045145-08894 C2_(6)5,895,495 36.09 BARC-044639-08743 C2_(6) 6,080,236 36.77BARCSOYSSR_06_0348 C2_(6) 6,288,376 37.43 Satt432 C2_(6) 6,288,376 37.43BARCSOYSSR_06_0362 C2_(6) 6,524,110 38.90 Satt281 C2_(6) 6,524,110 38.90BARC-027948-06704 C2_(6) 6,706,819 40.25 BARC-056271-14211 C2_(6)6,914,147 41.46 BARC-024221-04807 C2_(6) 7,072,465 41.51BARC-014321-01317 C2_(6) 7,190,150 42.30 BARC-031455-07095 C2_(6)7,313,010 42.54 BARCSOYSSR_06_0408 C2_(6) 7,320,698 42.94 Satt291 C2_(6)7,320,698 42.94 BARCSOYSSR_06_0473 C2_(6) 8,782,880 52.51 Satt457 C2_(6)8,782,880 52.51 BARCSOYSSR_06_0547 C2_(6) 10,231,895 57.29 Sat_153C2_(6) 10,231,895 57.29 BARC-029937-06757 C2_(6) 10,901,074 65.04BARC-040587-07787 C2_(6) 11,108,066 65.67 BARC-041867-08122 C2_(6)11,196,820 65.73 BARC-063259-18282 C2_(6) 11,337,217 66.09 S09155-1C2_(6) 11,659,627 69.29 BARC-024429-04882 C2_(6) 11,824,221 70.92BARC-018663-03235 C2_(6) 11,898,756 71.60 BARC-039613-07521 C2_(6)11,938,892 71.86 BARC-031571-07112 C2_(6) 12,129,054 72.39BARC-022299-04310 C2_(6) 12,273,626 72.39 BARCSOYSSR_06_0667 C2_(6)12,310,043 73.19 Satt322 C2_(6) 12,310,043 73.19 BARC-028177-05786C2_(6) 13,551,011 80.28 BARC-017285-02260 C2_(6) 13,674,273 81.14BARC-013837-01254 C2_(6) 14,247,199 86.27 BARC-052917-11675 C2_(6)14,272,287 86.96 BARC-016423-02585 C2_(6) 14,285,575 86.96BARC-014305-01308 C2_(6) 14,424,366 87.41 BARC-015081-02562 C2_(6)14,424,385 87.41 BARC-047715-10388 C2_(6) 14,849,172 88.14 S02037-1C2_(6) 15,457,913 89.19 BARCSOYSSR_06_0840 C2_(6) 15,756,463 89.71Satt363 C2_(6) 15,756,463 89.71 BARCSOYSSR_06_0850 C2_(6) 15,958,85990.53 Sat_076 C2_(6) 15,958,859 90.53 BARC-021735-04194 C2_(6)15,980,393 90.88 BARC-020031-04407 C2_(6) 16,050,227 91.43BARC-054075-12325 C2_(6) 16,050,267 92.10 BARCSOYSSR_06_0858 C2_(6)16,057,524 92.67 Satt643 C2_(6) 16,057,524 92.67 BARC-041165-07922C2_(6) 16,155,041 93.21 BARCSOYSSR_06_0876 C2_(6) 16,367,712 94.58Sat_402 C2_(6) 16,367,712 94.58 S13136-1 C2_(6) 16,391,391 94.84S17291-001 C2_(6) 16,499,786 96.04 S13139-1 C2_(6) 16,593,381 97.08BARC-025707-05008 C2_(6) 16,659,438 97.81 S17292-001 C2_(6) 16,670,04797.84 S13146-1 C2_(6) 16,804,435 98.23 BARC-056573-14503 C2_(6)16,914,099 98.55 BARC-063591-18406 C2_(6) 16,927,469 98.55BARC-013687-01230 C2_(6) 16,941,331 98.55 BARC-014491-01561 C2_(6)17,424,176 100.17 S17293-001 C2_(6) 17,498,270 100.29 BARC-064115-18558C2_(6) 17,899,364 100.94 BARC-020405-04602 C2_(6) 18,123,648 101.71S17294-001 C2_(6) 18,203,962 101.72 BARC-065853-19796 C2_(6) 18,860,236101.76 BARC-040213-07685 C2_(6) 18,953,546 101.85 S17581-001 C2_(6)19,743,496 102.13 S17691-001 C2_(6) 19,986,645 102.20 S17701-001 C2_(6)20,007,173 102.20 BARCSOYSSR_06_1041 C2_(6) 20,018,876 102.23 Satt557C2_(6) 20,018,876 102.23 S03703-1 C2_(6) 20,084,642 102.26 S17297-001C2_(6) 20,501,491 102.43 S17298-001 C2_(6) 21,197,184 102.71BARC-029239-06133 C2_(6) 21,487,556 102.83 S17299-001 C2_(6) 21,500,085102.83 BARC-054471-12090 C2_(6) 21,745,662 102.83 BARC-050867-09934C2_(6) 22,004,492 102.83 S17300-001 C2_(6) 22,501,610 102.93 S17301-001C2_(6) 22,700,011 102.97 BARCSOYSSR_06_1129 C2_(6) 23,874,403 103.22Satt489 C2_(6) 23,874,403 103.22 BARC-060711-16810 C2_(6) 25,068,452103.28 S17306-001 C2_(6) 25,700,006 103.29 BARC-057907-14996 C2_(6)27,768,566 103.30 S17310-001 C2_(6) 28,501,458 103.30 S17311-001 C2_(6)28,671,736 103.30 S17312-001 C2_(6) 29,499,523 103.30 S17313-001 C2_(6)30,203,054 103.31 S17316-001 C2_(6) 31,694,650 103.31 S17317-001 C2_(6)32,503,141 103.31 S17318-001 C2_(6) 33,196,184 103.32 BARCSOYSSR_06_1255C2_(6) 35,215,338 103.32 Sat_312 C2_(6) 35,215,338 103.32 S17322-001C2_(6) 35,509,548 103.37 BARC-024923-10366 C2_(6) 36,069,731 103.45S17326-001 C2_(6) 37,712,913 103.79 BARC-015077-02559 C2_(6) 38,136,028103.88 S17327-001 C2_(6) 38,467,854 104.00 S17328-001 C2_(6) 39,168,136104.25 S17329-001 C2_(6) 39,533,730 104.38 BARC-061147-17083 C2_(6)39,878,533 104.50 S10746-1 C2_(6) 40,766,974 104.94 BARC-056379-14289C2_(6) 41,204,571 105.16 BARC-029025-06051 C2_(6) 41,308,555 105.73S17331-001 C2_(6) 41,476,201 105.80 S17332-001 C2_(6) 42,450,296 106.19BARC-058239-15169 C2_(6) 42,603,052 106.26 BARC-011045-00827 C2_(6)42,963,664 106.36 BARC-059303-15722 C2_(6) 42,991,306 106.36BARC-023203-03824 C2_(6) 43,185,037 106.47 BARC-023277-05311 C2_(6)43,397,269 106.59 BARCSOYSSR_06_1476 C2_(6) 43,950,998 106.85 Satt079C2_(6) 43,950,998 106.85 BARC-051929-11299 C2_(6) 45,363,053 107.60BARC-062515-17881 C2_(6) 46,063,176 108.55 BARCSOYSSR_06_1579 C2_(6)46,273,201 109.58 Sct_028 C2_(6) 46,273,201 109.58 BARCSOYSSR_06_1581C2_(6) 46,286,900 109.96 Satt307 C2_(6) 46,286,900 109.96BARC-010777-00746 C2_(6) 47,413,265 113.05 S17337-001 C2_(6) 47,500,976113.10 S13093-1 C2_(6) 47,521,797 113.11 BARC-021425-04104 C2_(6)47,782,099 113.24 BARCSOYSSR_06_1680 C2_(6) 47,820,539 114.18 Satt202C2_(6) 47,820,539 114.18 S12211-1 C2_(6) 48,475,049 116.04BARCSOYSSR_06_1726 C2_(6) 48,582,450 116.34 Sat_252 C2_(6) 48,582,450116.34 BARC-038923-07396 C2_(6) 48,635,024 126.95 BARC-047703-10385C2_(6) 48,635,266 126.95 BARC-042663-08339 C2_(6) 48,658,985 126.95BARC-016969-02170 C2_(6) 48,677,811 126.95 BARCSOYSSR_06_1762 C2_(6)49,159,652 127.93 Satt371 C2_(6) 49,159,652 127.93 BARC-064859-18826C2_(6) 49,329,186 128.37 BARC-064297-18613 C2_(6) 49,411,956 129.53BARC-038861-07350 C2_(6) 49,975,437 132.41 S04555-1 C2_(6) 49,978,151132.43 BARC-025179-06455 C2_(6) 50,324,535 135.04 BARC-030551-06898C2_(6) 50,372,013 135.04 BARC-030551-06899 C2_(6) 50,372,013 136.12BARC-018915-03279 C2_(6) 50,602,830 136.51

TABLE 34 Locus LG (ch) Physical Genetic (cM) BARC-024147-04784 D1a_(1)398,072 0.00 BARC-028843-06027 D1a_(1) 507,545 5.38 S08519-1 D1a_(1)759,365 8.96 BARC-035199-07136 D1a_(1) 1,030,879 12.82 BARC-038883-07384D1a_(1) 1,490,280 15.98 BARC-045297-08928 D1a_(1) 1,744,924 16.72BARC-047699-10383 D1a_(1) 1,888,906 17.33 BARC-016475-02622 D1a_(1)2,205,640 18.59 BARC-015477-01982 D1a_(1) 2,280,958 19.67BARC-056093-14075 D1a_(1) 2,345,161 20.84 BARC-024477-04900 D1a_(1)2,699,581 24.80 BARC-042721-08396 D1a_(1) 3,318,354 26.90BARCSOYSSR_01_0206 D1a_(1) 3,758,425 31.67 Satt531 D1a_(1) 3,758,42531.67 BARC-030973-06982 D1a_(1) 4,324,690 33.54 BARC-060833-16926D1a_(1) 4,831,837 37.14

TABLE 35 Locus LG (ch) Physical Genetic (cM) BARC-029753-06334 D1b_(2)97,825 0.01 BARC-048593-10672 D1b_(2) 600,925 0.95 BARC-041773-08087D1b_(2) 653,480 3.54 BARC-032497-08984 D1b_(2) 841,950 4.85BARC-041475-08016 D1b_(2) 842,010 4.88 BARC-025791-05070 D1b_(2)1,071,624 5.75 BARC-013995-01298 D1b_(2) 1,893,325 12.38BARCSOYSSR_02_0106 D1b_(2) 1,974,569 14.06 Sat_279 D1b_(2) 1,974,56914.06 BARC-022263-04301 D1b_(2) 2,351,102 17.97 BARC-029969-06762D1b_(2) 2,454,222 18.80 BARC-029431-06192 D1b_(2) 2,903,075 19.78BARC-020103-04462 D1b_(2) 3,111,610 20.45 BARC-054295-12453 D1b_(2)3,295,143 21.46 BARC-032525-08992 D1b_(2) 3,469,712 21.96BARC-020481-04638 D1b_(2) 4,033,363 25.12 BARC-050661-09809 D1b_(2)4,190,107 26.14 BARC-018187-02537 D1b_(2) 4,344,986 27.01BARC-065787-19749 D1b_(2) 4,549,822 28.43 BARCSOYSSR_02_0263 D1b_(2)4,844,986 29.38 Sat_351 D1b_(2) 4,844,986 29.38 S12876-1 D1b_(2)4,893,148 29.48 BARC-046124-10284 D1b_(2) 5,319,977 30.39BARC-056237-14178 D1b_(2) 5,455,197 30.67 BARC-906883-01023 D1b_(2)5,555,734 30.67 BARC-051039-10958 D1b_(2) 5,900,203 32.40BARCSOYSSR_02_0339 D1b_(2) 6,307,499 34.56 Satt095 D1b_(2) 6,307,49934.56 BARC-048341-10551 D1b_(2) 6,660,140 36.12 BARC-041307-07962D1b_(2) 6,879,228 36.88 BARCSOYSSR_02_0385 D1b_(2) 6,977,734 37.46BE021153 D1b_(2) 6,977,734 37.46 BARC-028393-05861 D1b_(2) 7,260,55740.33 BARC-050325-09554 D1b_(2) 7,265,879 41.69 BARC-019149-03317D1b_(2) 7,472,850 42.10 BARC-019149-03315 D1b_(2) 7,472,850 44.25BARC-063497-18380 D1b_(2) 7,601,722 44.46 BARC-053459-11856 D1b_(2)8,172,878 45.03 BARCSOYSSR_02_0478 D1b_(2) 8,738,209 46.70 Satt698D1b_(2) 8,738,209 46.70 BARCSOYSSR_02_0480 D1b_(2) 8,742,635 46.70Sat_211 D1b_(2) 8,742,635 46.70 BARC-057545-14810 D1b_(2) 9,055,83346.85 BARC-062191-17700 D1b_(2) 9,094,347 47.08 BARCSOYSSR_02_0502D1b_(2) 9,385,720 47.44 Sat_173 D1b_(2) 9,385,720 47.44BARC-025955-05182 D1b_(2) 9,590,972 47.93 BARC-062989-18203 D1b_(2)9,714,336 48.44 S05937-1 D1b_(2) 9,714,426 48.44 BARC-016079-02059D1b_(2) 9,793,931 48.50 BARC-062943-18169 D1b_(2) 9,938,165 49.10BARC-030665-06919 D1b_(2) 10,233,955 50.25 BARCSOYSSR_02_0555 D1b_(2)10,538,050 52.98 Satt558 D1b_(2) 10,538,050 52.98 BARC-025183-06457D1b_(2) 10,630,472 53.70 BARCSOYSSR_02_0578 D1b_(2) 11,076,972 55.79Sat_254 D1b_(2) 11,076,972 55.79 BARCSOYSSR_02_0583 D1b_(2) 11,234,56758.22 AI856415 D1b_(2) 11,234,567 58.22 S08575-1 D1b_(2) 11,502,78058.78 BARCSOYSSR_02_0676 D1b_(2) 12,956,582 61.84 Satt542 D1b_(2)12,956,582 61.84 BARC-031301-07041 D1b_(2) 14,031,310 65.18BARC-048815-10726 D1b_(2) 14,106,291 66.18 BARC-013487-00500 D1b_(2)14,418,339 68.12 BARC-047945-10443 D1b_(2) 14,851,469 71.70 S08669-1D1b_(2) 15,446,229 76.53 BARC-043983-08572 D1b_(2) 15,490,882 76.90BARC-018819-03259 D1b_(2) 15,718,441 79.16 BARC-018781-03247 D1b_(2)15,718,559 79.16 BARC-027390-06561 D1b_(2) 16,502,802 79.17BARCSOYSSR_02_0846 D1b_(2) 17,474,784 81.46 Satt428 D1b_(2) 17,474,78481.46 BARCSOYSSR_02_0855 D1b_(2) 19,409,056 82.59 Satt579 D1b_(2)19,409,056 82.59 BARC-061653-17307 D1b_(2) 30,848,974 83.01BARCSOYSSR_02_1048 D1b_(2) 32,526,214 83.26 Satt600 D1b_(2) 32,526,21483.26 S11212-1 D1b_(2) 33,158,449 83.28 BARC-057711-14907 D1b_(2)36,102,833 83.35 BARC-052515-11484 D1b_(2) 38,644,397 83.36BARC-060135-16407 D1b_(2) 39,922,914 83.38 BARC-018381-03605 D1b_(2)40,362,445 83.93 BARC-049713-09132 D1b_(2) 40,552,642 84.11BARC-053163-11724 D1b_(2) 40,596,174 84.31 BARC-063685-18434 D1b_(2)40,623,295 84.31 BARC-053161-11723 D1b_(2) 40,704,043 84.69BARCSOYSSR_02_1257 D1b_(2) 40,884,780 85.66 Sat_169 D1b_(2) 40,884,78085.66 BARCSOYSSR_02_1268 D1b_(2) 41,290,043 87.01 Satt644 D1b_(2)41,290,043 87.01 BARC-032679-09011 D1b_(2) 41,923,345 88.86BARC-055839-13759 D1b_(2) 42,622,375 90.55 BARCSOYSSR_02_1386 D1b_(2)43,775,594 93.94 Satt546 D1b_(2) 43,775,594 93.94 BARC-018115-02528D1b_(2) 44,075,539 94.55 BARC-032025-07239 D1b_(2) 44,109,165 94.88BARC-024409-04868 D1b_(2) 44,522,551 95.29 BARC-021561-04146 D1b_(2)44,574,118 95.45 BARCSOYSSR_02_1436 D1b_(2) 44,879,014 98.37 Sat_139D1b_(2) 44,879,014 98.37 BARCSOYSSR_02_1500 D1b_(2) 45,655,561 103.25Satt703 D1b_(2) 45,655,561 103.25 BARC-030479-06875 D1b_(2) 45,682,686103.61 S00543-1 D1b_(2) 45,776,142 103.71 BARC-040187-07679 D1b_(2)45,948,050 103.90 BARC-021647-04164 D1b_(2) 46,042,031 103.90BARCSOYSSR_02_1540 D1b_(2) 46,353,760 105.87 Sat_069 D1b_(2) 46,353,760105.87 BARCSOYSSR_02_1602 D1b_(2) 47,404,748 113.32 Sat_183 D1b_(2)47,404,748 113.32 BARC-017895-02427 D1b_(2) 47,548,016 114.69BARC-045013-08865 D1b_(2) 48,138,016 116.48 BARC-028373-05856 D1b_(2)48,185,260 116.49 BARC-054149-12354 D1b_(2) 48,374,309 118.34BARCSOYSSR_02_1682 D1b_(2) 48,621,937 119.18 Sat_198 D1b_(2) 48,621,937119.18 BARC-057665-14892 D1b_(2) 48,703,378 120.41 BARC-040169-07675D1b_(2) 49,388,450 125.79 BARC-044747-08795 D1b_(2) 49,530,080 126.26BARC-054217-12380 D1b_(2) 49,541,234 126.26 BARCSOYSSR_02_1759 D1b_(2)50,122,136 129.78 Sat_289 D1b_(2) 50,122,136 129.78 BARC-059321-15931D1b_(2) 50,231,557 130.71 BARC-051677-11199 D1b_(2) 50,270,411 130.81BARC-039799-07588 D1b_(2) 50,691,457 131.85 BARC-019805-04379 D1b_(2)51,243,272 133.30 BARC-041469-08004 D1b_(2) 51,407,018 133.85BARC-020293-04543 D1b_(2) 51,541,368 134.02 BARC-906743-01012 D1b_(2)51,549,897 134.02

TABLE 36 Locus LG (ch) Physical Genetic (cM) BARC-012687-00367 D2_(17)8,987,706 42.45 BARCSOYSSR_17_0510 D2_(17) 9,088,821 42.69 Satt002D2_(17) 9,088,821 42.69 BARC-024449-04894 D2_(17) 9,260,050 44.74BARCSOYSSR_17_0554 D2_(17) 9,863,263 46.77 Satt154 D2_(17) 9,863,26346.77 BARCSOYSSR_17_0561 D2_(17) 9,949,913 47.18 Satt582 D2_(17)9,949,913 47.18 BARC-031145-07005 D2_(17) 10,534,591 50.41BARC-025885-05138 D2_(17) 11,157,614 55.59 BARC-025885-05137 D2_(17)11,157,614 55.78 BARC-017191-02247 D2_(17) 11,260,712 57.18BARC-063551-18386 D2_(17) 11,372,457 57.33 BARCSOYSSR_17_0669 D2_(17)11,724,512 58.74 Satt397 D2_(17) 11,724,512 58.74 BARC-013637-01186D2_(17) 11,915,457 59.92 BARC-013969-01290 D2_(17) 12,666,290 62.79BARCSOYSSR_17_0731 D2_(17) 12,771,421 62.88 Sat_292 D2_(17) 12,771,42162.88 BARCSOYSSR_17_0754 D2_(17) 13,150,232 63.94 Sat_222 D2_(17)13,150,232 63.94 BARC-047685-10379 D2_(17) 13,354,764 64.72BARCSOYSSR_17_0807 D2_(17) 14,024,929 68.20 Satt389 D2_(17) 14,024,92968.20 BARC-051665-11191 D2_(17) 14,849,946 72.14 BARC-047829-10399D2_(17) 14,938,405 72.23 BARC-048389-10562 D2_(17) 15,128,584 72.65BARC-059581-15926 D2_(17) 16,113,309 73.34 S01452-1 D2_(17) 16,136,64673.34 BARC-060511-16708 D2_(17) 17,995,210 73.34 BARC-062079-17648D2_(17) 18,355,304 73.34 BARC-062127-17661 D2_(17) 18,480,666 73.34BARCSOYSSR_17_0930 D2_(17) 18,770,886 73.91 Satt514 D2_(17) 18,770,88673.91 BARCSOYSSR_17_0973 D2_(17) 19,746,681 74.20 Satt082 D2_(17)19,746,681 74.20 BARCSOYSSR_17_0988 D2_(17) 20,710,130 74.25 Sat_300D2_(17) 20,710,130 74.25 BARC-010289-00577 D2_(17) 24,102,133 75.05BARC-028773-06009 D2_(17) 24,177,949 75.06 BARC-065605-19580 D2_(17)25,895,720 75.44 BARC-060353-16626 D2_(17) 27,486,421 75.44BARC-065169-19205 D2_(17) 28,115,010 75.44 BARC-065239-19278 D2_(17)31,882,561 75.85 BARC-057449-14753 D2_(17) 34,117,998 76.12BARC-050501-09705 D2_(17) 36,462,106 77.39 BARC-040583-07786 D2_(17)37,275,595 78.31 BARC-019787-04375 D2_(17) 37,418,900 78.52BARC-064095-18554 D2_(17) 37,769,021 79.94 BARC-037179-06731 D2_(17)38,089,554 82.62 BARCSOYSSR_17_1425 D2_(17) 38,091,254 84.17 GMHSP179D2_(17) 38,091,254 84.17 BARC-013653-01222 D2_(17) 38,730,417 86.45BARC-025927-05161 D2_(17) 38,916,720 87.84 BARCSOYSSR_17_1477 D2_(17)39,057,375 90.28 Satt310 D2_(17) 39,057,375 90.28 BARC-049255-10878D2_(17) 39,399,533 95.97 BARCSOYSSR_17_1511 D2_(17) 39,561,506 98.51Sat_326 D2_(17) 39,561,506 98.51 S11993-1 D2_(17) 39,804,515 99.75BARCSOYSSR_17_1540 D2_(17) 40,043,057 100.96 Satt413 D2_(17) 40,043,057100.96 BARC-010861-00784 D2_(17) 40,052,990 101.43 BARC-055793-13720D2_(17) 40,053,275 101.43 BARC-029859-06448 D2_(17) 40,146,564 104.31BARC-029279-06138 D2_(17) 41,007,685 109.10 BARC-014747-01639 D2_(17)41,146,946 110.80 BARC-019021-03292 D2_(17) 41,237,076 111.26BARCSOYSSR_17_1639 D2_(17) 41,333,788 114.29 Sat_220 D2_(17) 41,333,788114.29 BARC-039151-07458 D2_(17) 41,489,936 116.10 BARC-051411-11102D2_(17) 41,520,637 117.24 BARC-030531-06894 D2_(17) 41,806,677 117.79BARC-001489-00142 D2_(17) 41,821,321 118.12

TABLE 37 Locus LG (ch) Physical Genetic (cM) BARC-017755-03124 E_(15)11,798,929 59.38 BARC-018461-02916 E_(15) 12,256,121 61.36BARC-062799-18070 E_(15) 13,676,958 66.03 BARC-066103-17539 E_(15)13,735,240 66.03 BARC-057283-14667 E_(15) 13,762,803 68.06BARC-030079-06803 E_(15) 14,032,584 68.46 BARC-038377-10061 E_(15)14,329,242 69.39 BARC-054023-12243 E_(15) 14,753,749 69.79BARCSOYSSR_15_0692 E_(15) 14,918,775 70.47 Satt606 E_(15) 14,918,77570.47 BARC-054095-12332 E_(15) 15,100,427 70.60 BARC-016029-02040 E_(15)15,100,540 70.60 BARC-023525-05447 E_(15) 15,443,300 71.20BARC-060905-16966 E_(15) 15,743,043 71.42 BARCSOYSSR_15_0753 E_(15)16,668,418 72.02 Sat_136 E_(15) 16,668,418 72.02 BARCSOYSSR_15_0765E_(15) 17,025,474 74.32 Sat_380 E_(15) 17,025,474 74.32BARCSOYSSR_15_0766 E_(15) 17,054,779 74.37 Satt706 E_(15) 17,054,77974.37 BARC-029637-06273 E_(15) 17,582,453 74.81 BARCSOYSSR_15_0800E_(15) 17,692,405 75.28 Sat_107 E_(15) 17,692,405 75.28BARC-052575-11504 E_(15) 18,539,487 75.81 BARC-054787-12166 E_(15)19,024,123 75.94 BARC-059455-15814 E_(15) 20,019,884 76.10BARC-030059-06795 E_(15) 20,686,689 76.37 BARC-059689-16003 E_(15)21,179,215 76.60 BARC-061007-17001 E_(15) 22,274,650 76.87BARC-059873-16177 E_(15) 23,625,526 77.04 BARC-062747-18029 E_(15)30,330,055 77.04 BARC-059537-15899 E_(15) 32,251,236 77.04BARCSOYSSR_15_1125 E_(15) 34,902,080 77.04 Satt483 E_(15) 34,902,08077.04 BARC-039931-07614 E_(15) 36,577,083 77.27 BARC-063963-18516 E_(15)37,088,862 77.41 BARC-051429-11107 E_(15) 37,297,779 77.49BARC-058493-15308 E_(15) 39,652,366 78.62 BARC-007650-00171 E_(15)41,305,413 78.64 BARC-001485-00045 E_(15) 41,305,449 78.64BARC-014501-01563 E_(15) 41,841,189 78.66 BARC-044083-08609 E_(15)43,374,464 79.23 BARC-028805-06018 E_(15) 43,849,421 79.25BARC-028221-05799 E_(15) 43,851,079 79.27 BARC-050947-10881 E_(15)45,424,612 80.37 BARC-055571-13451 E_(15) 47,021,065 81.62BARC-055527-13350 E_(15) 47,080,727 82.28 BARC-051565-11166 E_(15)47,427,853 82.70 BARC-040965-07871 E_(15) 48,222,867 84.93BARC-016083-02061 E_(15) 48,657,557 85.49 BARC-043041-08509 E_(15)48,694,488 85.88 BARC-052379-11435 E_(15) 48,781,847 86.52BARC-020425-04614 E_(15) 48,863,918 86.64 BARC-016131-02290 E_(15)49,621,518 88.47 BARC-013073-00440 E_(15) 49,883,172 90.16BARC-022009-04249 E_(15) 50,061,005 91.30 BARC-042937-08466 E_(15)50,114,250 92.37 S13446-1 E_(15) 50,237,460 92.65 BARCSOYSSR_15_1568E_(15) 50,282,274 92.75 Sat_381 E_(15) 50,282,274 92.75BARC-013235-00458 E_(15) 50,334,269 93.35 BARC-025839-05112 E_(15)50,395,865 93.42 BARC-017767-03127 E_(15) 50,396,230 93.53BARCSOYSSR_15_1582 E_(15) 50,497,750 96.42 Satt231 E_(15) 50,497,75096.42

TABLE 38 Locus LG (ch) Physical Genetic (cM) S00252-1 F_(13) 235,4390.00 BARC-010699-00711 F_(13) 614,924 0.00 BARC-017209-02250 F_(13)730,833 5.44 BARCSOYSSR_13_0062 F_(13) 1,294,413 9.67 Satt659 F_(13)1,294,413 9.67 BARC-025291-06469 F_(13) 1,456,775 10.02BARCSOYSSR_13_0099 F_(13) 1,909,350 11.55 Sat_039 F_(13) 1,909,350 11.55BARC-027474-06587 F_(13) 2,028,114 11.77 BARC-032373-08957 F_(13)2,708,409 13.08 BARC-065403-19439 F_(13) 2,776,800 13.08BARC-051955-11307 F_(13) 3,140,575 15.04 BARC-064051-18538 F_(13)4,198,168 18.38 BARC-016463-02617 F_(13) 4,208,231 18.42BARC-051237-11031 F_(13) 4,227,643 18.55 BARC-051235-11030 F_(13)4,246,363 18.61 BARC-066191-19815 F_(13) 4,553,351 19.16BARC-035375-07174 F_(13) 4,556,823 19.18 BARC-059869-16174 F_(13)4,583,951 20.08 BARC-043267-08567 F_(13) 5,043,469 20.99BARCSOYSSR_13_0272 F_(13) 5,376,598 22.62 Satt252 F_(13) 5,376,598 22.62BARCSOYSSR_13_0282 F_(13) 5,491,280 23.35 Satt348 F_(13) 5,491,280 23.35BARC-013115-01441 F_(13) 6,069,736 24.26 BARCSOYSSR_13_0340 F_(13)6,580,549 27.45 Satt269 F_(13) 6,580,549 27.45 BARCSOYSSR_13_0341 F_(13)6,593,658 27.61 Satt145 F_(13) 6,593,658 27.61 BARC-042289-08234 F_(13)6,780,758 27.94 BARC-049723-09133 F_(13) 7,103,710 29.63BARC-051405-11095 F_(13) 7,521,465 31.01 BARC-058031-15072 F_(13)7,700,339 31.36 BARC-059611-15942 F_(13) 7,755,550 31.55BARC-046112-10273 F_(13) 7,858,072 32.14 BARC-043173-08548 F_(13)8,264,459 33.67 BARC-016943-02391 F_(13) 8,529,450 33.93BARC-018551-02971 F_(13) 8,529,473 34.07 BARCSOYSSR_13_0445 F_(13)8,722,718 34.39 Satt030 F_(13) 8,722,718 34.39 BARCSOYSSR_13_0458 F_(13)9,567,240 34.72 Satt569 F_(13) 9,567,240 34.72 BARC-064377-18635 F_(13)10,551,898 34.86 BARC-024749-05639 F_(13) 10,719,759 35.01BARC-023287-05318 F_(13) 10,722,785 35.01 BARCSOYSSR_13_0518 F_(13)11,494,492 35.29 Satt343 F_(13) 11,494,492 35.29 BARC-019391-03903F_(13) 11,513,020 35.44 BARC-014099-01531 F_(13) 11,513,023 35.44BARC-049859-09180 F_(13) 12,279,425 35.98 BARC-024639-05505 F_(13)12,952,996 36.54 BARC-064897-18988 F_(13) 13,803,730 36.66BARC-061105-17048 F_(13) 13,826,582 36.67 BARC-064849-18822 F_(13)17,609,468 36.68 BARC-062009-17616 F_(13) 19,330,460 36.74 S04060-1F_(13) 20,365,663 36.90 S02664-1 F_(13) 20,744,030 36.96BARC-044797-08809 F_(13) 23,987,460 37.47 BARCSOYSSR_13_0877 F_(13)24,451,400 39.62 Satt663 F_(13) 24,451,400 39.62 BARCSOYSSR_13_0952F_(13) 25,789,165 43.04 Sat_297 F_(13) 25,789,165 43.04BARC-050657-09804 F_(13) 26,009,844 45.03 BARC-025897-05144 F_(13)27,144,939 49.42 BARC-008001-00154 F_(13) 27,569,047 50.40BARC-038413-10074 F_(13) 27,781,754 50.71 BARCSOYSSR_13_1098 F_(13)28,415,998 51.20 Satt334 F_(13) 28,415,998 51.20 BARC-007567-00030F_(13) 29,549,705 52.26 BARC-041671-08065 F_(13) 30,268,846 53.20BARC-063863-18477 F_(13) 30,396,785 53.20 BARC-030853-06954 F_(13)30,581,858 54.08 BARC-047961-10449 F_(13) 30,582,406 54.08BARC-013633-01184 F_(13) 30,771,429 55.32 BARC-043227-08562 F_(13)30,863,656 55.99 BARC-015903-02010 F_(13) 30,965,576 56.03BARCSOYSSR_13_1241 F_(13) 30,984,460 56.89 Sat_317 F_(13) 30,984,46056.89 BARC-018079-02510 F_(13) 31,994,036 60.49 BARC-061189-17109 F_(13)32,064,753 64.12 BARC-039631-07532 F_(13) 32,179,461 65.09BARC-013257-00462 F_(13) 32,207,393 65.13 BARC-038503-10136 F_(13)32,623,088 66.91 BARC-041649-08056 F_(13) 33,280,536 68.55BARC-024045-04714 F_(13) 33,302,688 68.70 BARC-039765-07568 F_(13)33,302,789 68.73 BARCSOYSSR_13_1369 F_(13) 33,555,511 69.12 Sct_188F_(13) 33,555,511 69.12 BARC-047893-10417 F_(13) 33,591,576 69.33BARCSOYSSR_13_1385 F_(13) 33,860,249 69.98 Sat_375 F_(13) 33,860,24969.98 BARC-018605-02982 F_(13) 33,962,287 70.04 BARC-027502-06598 F_(13)34,222,888 71.11 BARC-032717-09021 F_(13) 34,437,496 71.22BARC-044875-08829 F_(13) 34,624,490 71.26 BARC-055229-13122 F_(13)34,739,895 71.89 BARC-031567-07110 F_(13) 34,841,259 71.89BARC-045235-08913 F_(13) 34,855,765 71.89 S00281-1 F_(13) 35,174,14073.16 BARC-018007-02494 F_(13) 35,393,757 74.03 BARC-063121-18247 F_(13)35,533,783 74.33 BARC-027622-06625 F_(13) 35,617,394 74.54BARC-025859-05126 F_(13) 35,862,469 75.44 BARC-018177-02535 F_(13)36,054,552 75.95 BARC-055613-13490 F_(13) 36,204,226 77.16BARCSOYSSR_13_1522 F_(13) 36,401,759 77.32 Sat_197 F_(13) 36,401,75977.32 BARC-025561-06521 F_(13) 36,822,800 78.34 BARC-014657-01608 F_(13)37,024,135 79.43 BARC-039175-07463 F_(13) 37,452,579 80.29BARC-027792-06674 F_(13) 38,023,035 85.18 BARC-046144-10286 F_(13)38,030,995 85.18 BARCSOYSSR_13_1617 F_(13) 38,075,339 87.79 Satt554F_(13) 38,075,339 87.79 BARCSOYSSR_13_1646 F_(13) 38,558,080 91.39Satt657 F_(13) 38,558,080 91.39 BARC-061571-17276 F_(13) 38,566,34891.63 BARC-063309-18328 F_(13) 38,566,921 91.63 BARCSOYSSR_13_1672F_(13) 38,955,502 93.73 Satt522 F_(13) 38,955,502 93.73BARC-026113-05263 F_(13) 39,216,776 95.85 BARC-038355-10050 F_(13)39,539,890 96.91 BARCSOYSSR_13_1747 F_(13) 40,160,823 98.17 AW756935F_(13) 40,160,823 98.17 BARC-013325-00483 F_(13) 40,685,775 99.37BARC-013325-00484 F_(13) 40,685,775 100.61 BARC-042953-08476 F_(13)41,219,915 102.16 BARCSOYSSR_13_1803 F_(13) 41,259,685 102.95 Sat_090F_(13) 41,259,685 102.95 BARCSOYSSR_13_1837 F_(13) 41,868,210 104.84Sat_417 F_(13) 41,868,210 104.84 BARCSOYSSR_13_1838 F_(13) 41,885,014106.55 Satt656 F_(13) 41,885,014 106.55 BARC-018741-02997 F_(13)41,885,841 107.33 BARC-014363-01336 F_(13) 42,334,157 108.26BARC-017179-02236 F_(13) 42,483,466 108.82 BARC-064221-18586 F_(13)42,797,894 111.07 BARC-050361-09572 F_(13) 42,797,918 111.08BARC-014299-01307 F_(13) 42,920,500 112.25 BARC-021845-04222 F_(13)43,826,000 116.89 BARC-028899-06036 F_(13) 44,238,149 118.26

TABLE 39 Locus LG (ch) Physical Genetic (cM) BARC-020027-04405 G_(18)181,064 0.00 BARC-052957-11678 G_(18) 187,414 0.00 BARC-064665-18774G_(18) 224,648 0.11 S01109-1 G_(18) 305,113 0.92 BARC-043197-08552G_(18) 305,200 0.92 BARC-060195-16470 G_(18) 470,340 1.64BARC-018387-03171 G_(18) 488,479 7.01 BARC-022431-04323 G_(18) 734,3607.43 BARC-020839-03962 G_(18) 981,378 8.12 BARC-900558-00952 G_(18)999,063 8.12 BARC-049013-10791 G_(18) 1,277,303 8.39 BARC-015371-01813G_(18) 1,431,827 8.63 BARCSOYSSR_18_0093 G_(18) 1,621,261 9.44 Sat_210G_(18) 1,621,261 9.44 BARC-048245-10515 G_(18) 1,718,204 9.94BARC-G00219-00248 G_(18) 1,726,610 9.96 BARCSOYSSR_18_0102 G_(18)1,736,324 10.10 Satt309 G_(18) 1,736,324 10.10 BARC-012285-01798 G_(18)1,945,192 11.01 BARC-010917-01706 G_(18) 1,955,436 11.09BARC-012289-01799 G_(18) 1,957,590 11.12 BARC-028299-05817 G_(18)1,958,726 11.86 BARC-061523-17249 G_(18) 1,979,049 12.10BARC-030055-06792 G_(18) 2,033,662 12.15 BARC-025777-05064 G_(18)2,296,490 12.92 BARCSOYSSR_18_0142 G_(18) 2,409,497 13.98 Sat_141 G_(18)2,409,497 13.98 BARC-004952-00267 G_(18) 2,664,887 14.20BARCSOYSSR_18_0158 G_(18) 2,665,098 14.70 Satt610 G_(18) 2,665,098 14.70BARC-047665-10370 G_(18) 2,833,064 15.97 BARC-047787-10396 G_(18)2,853,047 16.14 BARCSOYSSR_18_0177 G_(18) 3,162,740 17.19 Satt570 G_(18)3,162,740 17.19 BARC-014395-01348 G_(18) 3,448,063 19.48BARCSOYSSR_18_0195 G_(18) 3,603,119 20.57 AW734137 G_(18) 3,603,11920.57 BARC-003432-00279 G_(18) 3,643,846 21.48 BARCSOYSSR_18_0250 G_(18)4,692,375 22.22 Satt217 G_(18) 4,692,375 22.22 BARCSOYSSR_18_0257 G_(18)4,800,515 24.96 Satt235 G_(18) 4,800,515 24.96 BARCSOYSSR_18_0295 G_(18)5,330,646 29.20 Sat_315 G_(18) 5,330,646 29.20 BARCSOYSSR_18_0305 G_(18)5,470,147 31.02 Sat_290 G_(18) 5,470,147 31.02 BARCSOYSSR_18_0316 G_(18)5,675,379 32.88 Sat_131 G_(18) 5,675,379 32.88 BARCSOYSSR_18_0324 G_(18)5,890,285 35.43 Satt324 G_(18) 5,890,285 35.43 BARCSOYSSR_18_0348 G_(18)6,169,586 36.97 Sat_403 G_(18) 6,169,586 36.97 BARC-040265-07700 G_(18)7,275,891 39.86 BARC-901121-00988 G_(18) 8,415,710 40.41BARC-063985-18522 G_(18) 8,791,883 40.41 BARC-039993-07626 G_(18)9,012,214 40.81 BARCSOYSSR_18_0550 G_(18) 11,400,889 43.03 Sat_308G_(18) 11,400,889 43.03 BARC-053419-11845 G_(18) 12,638,074 44.99BARC-056521-14449 G_(18) 14,167,067 47.51 BARC-059783-16090 G_(18)14,285,415 47.51 BARC-054849-12183 G_(18) 14,335,308 47.51BARC-049885-09225 G_(18) 14,570,865 48.21 BARC-064283-18606 G_(18)14,893,358 48.21 BARC-017647-02654 G_(18) 15,242,485 48.33BARC-059485-15839 G_(18) 15,676,568 48.95 BARC-040485-07753 G_(18)15,723,524 48.95 BARC-018333-03580 G_(18) 16,483,354 50.04BARC-018333-03581 G_(18) 16,483,354 50.24 BARC-019465-03616 G_(18)16,505,062 50.88 BARC-013677-01228 G_(18) 16,668,537 52.04BARC-061001-16998 G_(18) 16,797,216 52.04 BARC-047404-12924 G_(18)17,550,827 52.04 BARC-046912-12782 G_(18) 17,553,931 52.04BARC-046994-12826 G_(18) 17,575,698 52.04 BARC-046874-12778 G_(18)17,592,240 52.04 BARC-046872-12776 G_(18) 17,600,728 52.04BARC-046920-12786 G_(18) 17,603,029 52.04 BARC-046930-12795 G_(18)17,611,727 52.04 BARC-046926-12788 G_(18) 17,626,176 52.04BARC-046922-12787 G_(18) 17,630,432 52.04 BARC-057295-14678 G_(18)17,781,283 52.04 BARC-020159-04488 G_(18) 17,925,069 52.04BARC-060837-16930 G_(18) 18,410,099 52.04 BARC-058413-15279 G_(18)20,526,141 53.38 BARC-060825-16919 G_(18) 21,121,950 54.45BARC-047150-12874 G_(18) 21,364,220 54.45 BARC-047112-12860 G_(18)21,365,038 54.45 BARC-047096-12838 G_(18) 21,384,584 54.45BARC-063705-18440 G_(18) 21,701,030 54.45 BARC-055557-13432 G_(18)21,724,083 54.45 BARC-062097-17654 G_(18) 22,120,170 54.45BARCSOYSSR_18_0845 G_(18) 22,150,302 54.97 Satt303 G_(18) 22,150,30254.97 BARC-060189-16468 G_(18) 22,483,339 55.60 BARC-047504-12947 G_(18)22,535,676 55.60 BARC-061785-17386 G_(18) 22,585,948 55.60BARC-047502-12946 G_(18) 22,588,708 55.60 BARC-047102-12842 G_(18)22,603,647 55.60 BARC-055855-13794 G_(18) 23,123,288 55.60BARC-061111-17050 G_(18) 24,129,395 55.60 BARC-058369-15257 G_(18)27,610,750 55.60 BARC-060613-16749 G_(18) 27,931,082 55.60BARC-013825-01251 G_(18) 30,313,907 55.60 BARC-061647-17305 G_(18)31,080,816 55.60 BARC-056139-14122 G_(18) 31,828,672 55.60BARC-059397-15790 G_(18) 33,110,626 55.60 BARC-062783-18056 G_(18)33,753,070 55.60 BARC-030691-06926 G_(18) 34,178,194 55.60BARC-057565-14836 G_(18) 34,232,818 55.60 BARC-056267-14204 G_(18)36,963,309 55.60 BARC-061197-17134 G_(18) 39,413,323 55.60BARC-051485-11122 G_(18) 39,512,471 55.60 BARC-014783-01660 G_(18)41,560,487 55.60 BARC-061717-17358 G_(18) 41,730,041 55.60BARC-044235-08650 G_(18) 42,206,429 55.60 BARC-059239-15686 G_(18)43,529,731 56.18 BARC-056035-13999 G_(18) 45,468,441 56.71BARC-050493-09699 G_(18) 45,951,229 56.82 BARCSOYSSR_18_1146 G_(18)46,265,580 57.07 Satt533 G_(18) 46,265,580 57.07 BARCSOYSSR_18_1210G_(18) 48,532,689 57.82 Satt504 G_(18) 48,532,689 57.82BARCSOYSSR_18_1348 G_(18) 52,189,343 59.89 Sat_185 G_(18) 52,189,34359.89 BARCSOYSSR_18_1349 G_(18) 52,210,836 59.90 Sat_203 G_(18)52,210,836 59.90 BARCSOYSSR_18_1364 G_(18) 52,465,758 60.60 Satt199G_(18) 52,465,758 60.60 BARCSOYSSR_18_1385 G_(18) 52,746,490 60.97Sat_260 G_(18) 52,746,490 60.97 BARCSOYSSR_18_1418 G_(18) 53,445,94263.44 Satt012 G_(18) 53,445,942 63.44 BARC-056635-14538 G_(18)53,471,513 63.92 BARCSOYSSR_18_1426 G_(18) 53,656,489 65.78 Sat_164G_(18) 53,656,489 65.78 BARCSOYSSR_18_1431 G_(18) 53,769,539 66.39Satt517 G_(18) 53,769,539 66.39 BARC-027694-06635 G_(18) 54,764,50867.91 BARC-050613-09770 G_(18) 54,942,320 69.50 BARC-024489-04936 G_(18)55,001,002 70.62 BARC-055139-13077 G_(18) 55,458,709 71.46BARC-061783-18883 G_(18) 55,506,257 72.02 BARC-048761-10703 G_(18)56,086,706 72.84 BARC-016867-02359 G_(18) 56,429,486 73.34BARC-018441-03188 G_(18) 56,429,542 73.80 BARC-052045-11324 G_(18)57,071,922 75.00 BARC-026013-05225 G_(18) 57,185,832 75.64BARC-015063-02553 G_(18) 57,353,963 76.88 BARC-008223-00022 G_(18)57,436,269 78.05 BARC-032277-08935 G_(18) 57,462,526 79.40BARC-041705-08069 G_(18) 57,781,784 80.96 BARC-032785-09037 G_(18)57,781,833 80.96 S13844-1 G_(18) 58,086,324 85.55 BARCSOYSSR_18_1703G_(18) 58,093,491 85.66 Sct_199 G_(18) 58,093,491 85.66BARCSOYSSR_18_1708 G_(18) 58,136,286 85.98 Satt472 G_(18) 58,136,28685.98 BARC-048095-10484 G_(18) 58,177,377 86.59 BARC-038873-07372 G_(18)58,438,994 87.30 BARCSOYSSR_18_1750 G_(18) 58,722,839 89.37 Satt191G_(18) 58,722,839 89.37 BARCSOYSSR_18_1767 G_(18) 58,879,563 91.08Sat_117 G_(18) 58,879,563 91.08 BARC-010491-00654 G_(18) 59,279,44493.00 BARC-010495-00656 G_(18) 59,283,702 93.23 BARC-024251-04812 G_(18)59,472,425 94.30 BARC-020069-04425 G_(18) 59,797,088 96.31BARC-062677-18004 G_(18) 59,995,654 97.32 BARC-062769-18043 G_(18)60,441,813 100.16 BARCSOYSSR_18_1853 G_(18) 60,463,067 100.37 Sct_187G_(18) 60,463,067 100.37 BARC-044363-08678 G_(18) 60,487,624 100.44BARCSOYSSR_18_1858 G_(18) 60,612,599 101.82 Sat_064 G_(18) 60,612,599101.82 BARC-054735-12156 G_(18) 60,802,269 102.33 BARC-013647-01216G_(18) 60,909,921 103.22 BARC-055537-13406 G_(18) 61,041,397 103.40BARC-039397-07314 G_(18) 61,188,102 103.55 BARC-043995-08576 G_(18)61,306,670 104.09 BARC-064703-18782 G_(18) 61,480,202 105.53BARC-049989-09280 G_(18) 61,591,089 105.85 S05058-1 G_(18) 61,591,142105.85 S04660-1 G_(18) 61,831,970 106.50 BARC-017669-03102 G_(18)62,046,576 107.09

TABLE 40 Locus LG (ch) Physical Genetic (cM) BARC-030145-06814 H_(12)5,407,750 33.89 BARCSOYSSR_12_0301 H_(12) 5,945,172 40.93 Satt192 H_(12)5,945,172 40.93 BARC-020263-04537 H_(12) 6,151,630 42.24BARCSOYSSR_12_0320 H_(12) 6,361,611 43.39 Satt442 H_(12) 6,361,611 43.39BARC-041917-08135 H_(12) 6,370,716 43.68 BARC-055349-13226 H_(12)6,621,623 45.18 BARC-044091-08619 H_(12) 6,846,615 46.92BARC-018437-03181 H_(12) 7,430,953 49.44 BARC-014937-01927 H_(12)7,559,662 50.56 BARC-018477-03197 H_(12) 7,580,895 50.56BARC-011573-00291 H_(12) 7,708,831 51.54 BARC-032147-07327 H_(12)7,942,630 52.74 BARCSOYSSR_12_0484 H_(12) 9,096,372 55.66 Sat_334 H_(12)9,096,372 55.66 BARC-050381-09573 H_(12) 9,333,744 56.14BARC-063305-18323 H_(12) 9,470,906 56.16 BARC-018577-02980 H_(12)10,342,254 57.76 BARC-062921-18158 H_(12) 10,442,496 57.76BARC-050237-09522 H_(12) 11,092,912 58.34 BARC-050239-09523 H_(12)11,096,770 58.60 S09955-1 H_(12) 11,512,115 58.82 BARC-055493-13324H_(12) 16,472,555 61.44 BARC-056309-14242 H_(12) 16,472,572 61.45BARC-062469-17821 H_(12) 17,814,132 61.53 BARC-060801-16905 H_(12)17,818,053 61.54 BARCSOYSSR_12_0796 H_(12) 18,644,153 63.30 Satt253H_(12) 18,644,153 63.30 BARCSOYSSR_12_0933 H_(12) 27,755,144 63.49Satt279 H_(12) 27,755,144 63.49 BARCSOYSSR_12_1006 H_(12) 32,468,26064.59 Sat_205 H_(12) 32,468,260 64.59 BARCSOYSSR_12_1008 H_(12)32,497,101 65.39 Satt676 H_(12) 32,497,101 65.39 BARCSOYSSR_12_1065H_(12) 33,808,521 68.67 Satt629 H_(12) 33,808,521 68.67BARCSOYSSR_12_1068 H_(12) 33,904,742 69.47 Sat_158 H_(12) 33,904,74269.47 BARC-014455-01377 H_(12) 34,233,214 73.09 BARC-021753-04197 H_(12)34,421,276 74.86 BARC-044073-08598 H_(12) 34,428,011 74.86BARC-017975-02490 H_(12) 34,693,967 75.36 BARC-031017-06986 H_(12)34,778,965 75.59 BARC-051831-11255 H_(12) 34,896,373 77.45BARC-055767-13699 H_(12) 34,981,769 78.30 BARC-039403-07492 H_(12)35,019,859 78.39 BARC-050003-09283 H_(12) 35,088,372 78.39BARCSOYSSR_12_1142 H_(12) 35,108,116 78.95 Satt302 H_(12) 35,108,11678.95 BARC-021693-04179 H_(12) 35,195,967 79.70 BARC-064633-18761 H_(12)35,317,729 81.36 BARC-032397-08964 H_(12) 35,442,153 81.66BARC-044357-08676 H_(12) 35,442,160 81.67 BARCSOYSSR_12_1175 H_(12)35,565,380 82.68 Satt637 H_(12) 35,565,380 82.68 BARC-049209-10821H_(12) 35,718,223 83.15 BARC-019331-03879 H_(12) 36,046,607 84.20BARC-017985-02493 H_(12) 36,162,584 84.21 BARC-050707-09846 H_(12)36,518,632 85.62 BARCSOYSSR_12_1229 H_(12) 36,600,716 86.22 Sat_175H_(12) 36,600,716 86.22 BARC-015079-02561 H_(12) 36,780,206 89.38

TABLE 41 Locus LG (ch) Physical Genetic (cM) BARC-017193-02248 I_(20)33,440,941 40.09 BARC-015861-02878 I_(20) 34,090,779 41.90BARC-026051-05237 I_(20) 34,101,285 42.31 BARCSOYSSR_20_0803 I_(20)34,223,200 42.60 Satt270 I_(20) 34,223,200 42.60 BARC-060119-16401I_(20) 34,288,590 43.26 BARC-029461-06196 I_(20) 34,439,725 43.99BARC-039067-07437 I_(20) 34,505,216 44.00 BARC-024125-04772 I_(20)34,670,085 44.27 BARC-017311-02261 I_(20) 34,670,172 44.34BARC-055423-13277 I_(20) 34,916,007 44.95 BARC-025913-05152 I_(20)35,186,441 46.14 BARC-025913-05155 I_(20) 35,186,441 49.13BARC-050455-09643 I_(20) 35,480,417 49.93 BARC-029803-06418 I_(20)35,760,720 50.85 BARC-025987-05207 I_(20) 36,254,964 53.77BARC-024031-04707 I_(20) 36,260,991 53.77 BARC-016541-02090 I_(20)36,299,485 55.24 BARCSOYSSR_20_0935 I_(20) 36,694,570 56.11 Sat_104I_(20) 36,694,570 56.11 BARC-041445-07985 I_(20) 37,025,923 57.46BARC-048283-10541 I_(20) 37,239,375 59.44 BARC-020019-04404 I_(20)37,240,160 59.44 BARC-025847-05113 I_(20) 37,342,870 60.00BARC-017939-02461 I_(20) 37,645,405 60.30 BARC-039753-07565 I_(20)37,996,627 64.00 BARCSOYSSR_20_1041 I_(20) 38,389,919 66.82 Sat_418I_(20) 38,389,919 66.82 BARCSOYSSR_20_1053 I_(20) 38,657,712 67.56Sat_170 I_(20) 38,657,712 67.56 BARC-053725-11957 I_(20) 38,960,00070.92 S08034-1 I_(20) 39,051,858 71.47 BARC-022381-04318 I_(20)39,289,431 72.90 BARC-041051-07902 I_(20) 39,521,589 74.61BARC-029151-06100 I_(20) 39,900,787 76.68 BARCSOYSSR_20_1170 I_(20)40,299,039 78.82 Satt162 I_(20) 40,299,039 78.82 BARCSOYSSR_20_1227I_(20) 41,048,634 84.61 Satt623 I_(20) 41,048,634 84.61 S10293-1 I_(20)41,216,234 85.10 BARC-044361-08677 I_(20) 41,309,309 85.38BARC-025815-05092 I_(20) 41,492,675 87.03 BARC-045029-08866 I_(20)41,705,956 88.64 BARC-027542-06603 I_(20) 41,803,540 89.73BARCSOYSSR_20_1271 I_(20) 41,816,857 89.76 Sat_420 I_(20) 41,816,85789.76 BARCSOYSSR_20_1273 I_(20) 41,836,507 89.76 Sat_419 I_(20)41,836,507 89.76 BARC-042685-08348 I_(20) 41,982,978 90.45BARC-007970-00180 I_(20) 42,348,122 91.74 BARC-060361-16629 I_(20)42,397,180 92.03 BARCSOYSSR_20_1312 I_(20) 42,518,153 92.22 Sat_299I_(20) 42,518,153 92.22 BARCSOYSSR_20_1319 I_(20) 43,370,538 96.80AQ851518 I_(20) 43,370,538 96.80 BARC-055173-13105 I_(20) 43,686,51597.41 BARC-015569-02005 I_(20) 44,042,061 99.91 BARC-055331-13213 I_(20)44,397,389 103.80 BARC-042389-08249 I_(20) 44,488,499 104.76BARC-029707-06329 I_(20) 44,590,034 105.09 BARC-021793-04213 I_(20)44,790,257 105.66 BARC-016665-02164 I_(20) 44,817,525 105.67BARC-014559-01579 I_(20) 44,848,445 106.09 BARC-051303-11083 I_(20)44,947,571 106.93 BARC-051301-11081 I_(20) 44,947,600 106.93BARC-062771-18047 I_(20) 45,428,117 109.07 BARCSOYSSR_20_1322 I_(20)45,550,639 109.27 Sct_189 I_(20) 45,550,639 109.27 BARC-050097-09382I_(20) 45,627,350 109.40 BARCSOYSSR_20_1323 I_(20) 45,659,683 109.55Satt440 I_(20) 45,659,683 109.55 BARC-052289-11404 I_(20) 45,686,195109.58 BARC-063851-18472 I_(20) 45,794,065 110.09 BARC-017873-02409I_(20) 45,939,159 110.44 BARC-015559-02004 I_(20) 46,031,805 110.64BARC-028901-06041 I_(20) 46,108,591 110.85 BARC-048041-10476 I_(20)46,127,952 111.28 BARC-048631-10683 I_(20) 46,135,344 111.28BARC-055209-13116 I_(20) 46,596,717 112.77

TABLE 42 Locus LG (ch) Physical Genetic (cM) BARC-016027-02038 J_(16)133,348 2.34 BARC-028423-05867 J_(16) 724,502 4.91 BARC-013639-01204J_(16) 774,054 5.42 BARC-063377-18348 J_(16) 1,061,926 8.18BARC-024473-04898 J_(16) 1,103,589 8.58 BARCSOYSSR_16_0062 J_(16)1,141,072 10.55 Satt249 J_(16) 1,141,072 10.55 BARC-013651-01218 J_(16)1,348,520 11.40 BARCSOYSSR_16_0083 J_(16) 1,543,289 12.13 Satt674 J_(16)1,543,289 12.13 BARCSOYSSR_16_0090 J_(16) 1,631,806 12.21 Satt287 J_(16)1,631,806 12.21 BARC-018981-03289 J_(16) 2,314,419 19.26BARCSOYSSR_16_0171 J_(16) 2,893,992 22.52 Sct_046 J_(16) 2,893,992 22.52BARCSOYSSR_16_0179 J_(16) 3,050,011 22.97 Sat_228 J_(16) 3,050,011 22.97BARC-028599-05966 J_(16) 3,137,659 23.17 BARC-059355-15761 J_(16)3,363,314 24.28 BARC-042521-08287 J_(16) 3,534,838 24.37BARC-013299-00471 J_(16) 3,597,317 24.82 BARC-014573-01581 J_(16)3,597,402 24.82 BARC-018093-02513 J_(16) 3,847,598 25.29BARC-045157-08897 J_(16) 3,900,245 25.35 BARC-014467-01559 J_(16)3,962,333 25.69 S03813-1 J_(16) 4,678,569 30.57 BARC-029477-06200 J_(16)4,763,389 31.14 BARC-031525-07106 J_(16) 4,924,406 34.78BARC-031195-07010 J_(16) 4,924,462 34.78 BARC-028307-05823 J_(16)4,936,902 34.78 BARC-031951-07227 J_(16) 4,936,964 34.94BARC-065799-19753 J_(16) 5,040,869 35.44 BARCSOYSSR_16_0377 J_(16)6,273,768 38.03 Satt693 J_(16) 6,273,768 38.03 BARC-018889-03032 J_(16)6,474,327 38.62 BARCSOYSSR_16_0424 J_(16) 7,054,261 40.67 Sat_370 J_(16)7,054,261 40.67 BARC-028159-05778 J_(16) 7,070,781 41.63BARC-059919-16214 J_(16) 7,165,978 42.08 BARC-053335-11801 J_(16)7,237,770 42.31 BARC-048299-10543 J_(16) 7,446,239 43.04BARC-060769-16868 J_(16) 9,593,463 44.34 BARC-058125-15101 J_(16)10,818,091 44.60 BARC-058115-15097 J_(16) 13,368,263 44.60BARC-058941-15515 J_(16) 14,534,998 44.60 BARC-060857-16934 J_(16)14,887,272 44.61 BARC-056593-14514 J_(16) 15,091,717 44.61BARC-052587-11515 J_(16) 15,536,387 44.61 BARC-062281-17737 J_(16)16,322,634 44.61 BARC-025801-05075 J_(16) 16,552,294 44.61BARC-059701-16014 J_(16) 19,326,141 44.61 BARC-038343-10046 J_(16)19,423,620 44.61 BARC-013151-01456 J_(16) 20,512,221 44.61BARC-010869-00787 J_(16) 21,152,273 44.61 BARC-051521-11150 J_(16)21,264,807 44.61 BARCSOYSSR_16_0703 J_(16) 23,096,039 45.66 Satt529J_(16) 23,096,039 45.66 BARC-059377-15777 J_(16) 25,697,824 46.05BARCSOYSSR_16_0803 J_(16) 26,813,827 46.10 Sat_165 J_(16) 26,813,82746.10 BARCSOYSSR_16_0840 J_(16) 27,633,714 46.11 Satt622 J_(16)27,633,714 46.11 BARCSOYSSR_16_0885 J_(16) 28,589,375 47.36 Satt215J_(16) 28,589,375 47.36 BARC-029037-06053 J_(16) 29,156,483 51.57BARC-038949-07404 J_(16) 30,065,357 57.70 BARC-059837-16121 J_(16)30,151,468 58.39 BARC-042193-08207 J_(16) 30,395,923 62.96BARC-032663-09006 J_(16) 30,962,138 65.78 BARC-017697-03107 J_(16)31,075,508 66.45 BARC-024047-04716 J_(16) 31,105,844 66.47BARC-022077-04282 J_(16) 31,154,859 66.56 BARC-014795-01662 J_(16)31,155,317 66.56 BARC-042895-08450 J_(16) 31,292,648 67.05BARC-043111-08534 J_(16) 31,461,544 67.48 BARC-060179-16450 J_(16)31,613,798 67.74 BARC-011645-00322 J_(16) 31,635,367 67.90BARCSOYSSR_16_1073 J_(16) 31,795,061 68.81 Sctt011 J_(16) 31,795,06168.81 BARC-010297-00580 J_(16) 31,996,027 69.90 BARC-017835-02393 J_(16)32,526,995 71.32 BARC-012971-00414 J_(16) 32,573,581 71.56BARC-024115-04764 J_(16) 32,962,414 71.92 BARC-040393-07727 J_(16)33,410,287 73.26 BARC-025217-06463 J_(16) 33,513,918 73.90BARCSOYSSR_16_1165 J_(16) 33,538,157 74.90 Satt547 J_(16) 33,538,15774.90 BARC-028589-05965 J_(16) 33,853,031 76.14 BARC-053847-12078 J_(16)34,475,602 77.27 BARC-051715-11216 J_(16) 35,032,380 77.40BARC-045099-08885 J_(16) 35,208,435 78.97 BARC-025851-05117 J_(16)35,571,437 80.79 BARC-044031-08587 J_(16) 35,587,464 81.41BARCSOYSSR_16_1234 J_(16) 35,718,507 82.03 Satt431 J_(16) 35,718,50782.03 BARC-045133-08889 J_(16) 36,163,500 84.07 BARC-015307-02272 J_(16)36,221,550 84.76 S02042-1 J_(16) 36,524,407 85.53 BARC-011625-00310J_(16) 36,544,211 85.58 BARC-024229-04809 J_(16) 36,641,788 86.17BARC-048135-10500 J_(16) 36,732,539 86.82 BARC-019219-03397 J_(16)36,921,370 87.38 BARC-030203-06832 J_(16) 37,108,010 87.58BARC-029163-06102 J_(16) 37,181,366 88.51 BARC-030817-06946 J_(16)37,289,136 88.93

TABLE 43 Locus LG (ch) Physical Genetic (cM) BARCSOYSSR_19_1128 L_(19)41,423,108 55.66 Satt076 L_(19) 41,423,108 55.66 BARC-055739-13676L_(19) 42,048,498 59.18 BARCSOYSSR_19_1176 L_(19) 42,110,356 59.44Sat_113 L_(19) 42,110,356 59.44 BARCSOYSSR_19_1213 L_(19) 42,830,78161.40 Satt678 L_(19) 42,830,781 61.40 BARC-047494-12937 L_(19)42,846,587 61.48 BARC-011641-00318 L_(19) 42,955,778 61.87BARC-044913-08839 L_(19) 43,125,513 62.31 BARCSOYSSR_19_1251 L_(19)43,523,563 69.12 Sat_099 L_(19) 43,523,563 69.12 BARC-044465-08706L_(19) 44,175,110 72.22 BARC-035235-07156 L_(19) 44,566,701 74.76BARC-013505-00505 L_(19) 44,810,522 76.10 BARCSOYSSR_19_1329 L_(19)44,978,924 77.47 Sat_286 L_(19) 44,978,924 77.47 BARC-029975-06765L_(19) 45,144,453 78.09 BARC-013007-00419 L_(19) 45,472,890 79.01BARC-021733-04193 L_(19) 45,993,209 80.75 BARCSOYSSR_19_1381 L_(19)46,001,862 81.03 Satt006 L_(19) 46,001,862 81.03 BARCSOYSSR_19_1383L_(19) 46,109,715 81.33 Satt664 L_(19) 46,109,715 81.33BARC-014655-01607 L_(19) 46,478,087 84.05 BARC-030101-06809 L_(19)46,516,411 84.05 BARC-029419-06181 L_(19) 46,611,807 84.53BARC-028787-06014 L_(19) 46,761,021 85.15 BARC-022199-04295 L_(19)46,811,335 85.15 BARC-015493-01985 L_(19) 46,811,560 85.20BARC-064839-18815 L_(19) 47,117,038 86.12 BARC-021321-04035 L_(19)47,258,614 86.15 S16601-001 L_(19) 47,535,046 87.73 BARC-018175-02534L_(19) 47,721,962 88.79 S01481-1 L_(19) 47,826,727 89.53BARC-055107-13809 L_(19) 47,867,062 89.81 BARC-055773-13715 L_(19)48,037,516 90.42 BARC-013129-01447 L_(19) 48,074,048 90.44BARC-013053-00429 L_(19) 48,174,962 90.85 S11309-1 L_(19) 48,252,04091.10 BARC-052179-11387 L_(19) 48,307,020 91.27 BARC-027414-06567 L_(19)48,407,210 91.61 S11320-1 L_(19) 48,638,646 92.18 BARC-030273-06844L_(19) 49,088,662 93.28 BARCSOYSSR_19_1543 L_(19) 49,191,367 93.95Satt373 L_(19) 49,191,367 93.95 BARC-051673-11193 L_(19) 49,340,37894.04 BARC-041915-08133 L_(19) 49,845,318 99.11 BARCSOYSSR_19_1580L_(19) 50,023,695 101.14 Sat_245 L_(19) 50,023,695 101.14 S04040-1L_(19) 50,222,676 100.89 BARC-028353-05838 L_(19) 50,302,422 100.79BARC-042699-08377 L_(19) 50,414,357 100.58 BARC-019039-03054 L_(19)50,424,707 99.67

TABLE 44 Locus LG (ch) Physical Genetic (cM) BARCSOYSSR_07_0017 M_(7)220,579 1.17 Satt404 M_(7) 220,579 1.17 BARC-059421-15798 M_(7) 226,5374.97 BARC-015439-01969 M_(7) 376,594 5.47 BARC-008017-00148 M_(7)580,840 6.81 S00863-1 M_(7) 1,141,099 8.09 BARCSOYSSR_07_0075 M_(7)1,201,859 8.23 Satt636 M_(7) 1,201,859 8.23 BARC-044075-08603 M_(7)1,421,872 8.57 BARC-029703-06326 M_(7) 1,628,392 10.60 S17151-001 M_(7)1,830,296 11.64 S17153-001 M_(7) 1,923,026 12.12 BARCSOYSSR_07_0109M_(7) 2,006,120 12.55 Satt201 M_(7) 2,006,120 12.55 BARC-039741-07564M_(7) 2,041,844 12.66 S17154-001 M_(7) 2,179,883 13.97 BARC-042621-08316M_(7) 2,196,306 14.13 BARC-035447-07202 M_(7) 2,279,904 15.14 S17156-001M_(7) 2,310,058 15.53 BARCSOYSSR_07_0134 M_(7) 2,414,495 16.86 Satt150M_(7) 2,414,495 16.86 BARC-025961-05189 M_(7) 2,477,005 17.71 S17159-001M_(7) 2,679,749 18.14 BARC-061549-17261 M_(7) 2,737,694 18.27BARC-059899-16208 M_(7) 2,924,066 18.54 S08590-1 M_(7) 3,009,018 19.96BARC-042631-08332 M_(7) 3,184,418 22.91 BARC-054347-12492 M_(7)3,301,644 24.46 BARC-013845-01256 M_(7) 3,598,752 27.93BARC-050315-09547 M_(7) 4,241,757 31.48 S17242-001 M_(7) 4,282,676 31.68S17166-001 M_(7) 4,319,368 31.87 S17167-001 M_(7) 4,342,479 31.99BARC-015945-02020 M_(7) 4,380,782 32.18 BARC-012947-00412 M_(7)4,380,831 32.18 BARCSOYSSR_07_0247 M_(7) 4,510,496 32.75 Satt567 M_(7)4,510,496 32.75 BARCSOYSSR_07_0263 M_(7) 4,963,009 34.27 Satt540 M_(7)4,963,009 34.27 S08539-1 M_(7) 5,576,650 36.74 BARC-028455-05917 M_(7)5,899,369 38.05 BARC-044469-08707 M_(7) 6,036,308 38.74BARC-050461-09646 M_(7) 6,209,838 39.88 S17178-001 M_(7) 6,288,899 40.59BARC-055563-13436 M_(7) 6,302,756 40.72 S17179-001 M_(7) 6,340,656 40.83S17180-001 M_(7) 6,347,675 40.85 BARC-039195-07465 M_(7) 6,528,733 41.37S17181-001 M_(7) 6,614,649 41.66 S17182-001 M_(7) 6,616,695 41.66S17183-001 M_(7) 6,623,333 41.69 S02780-1 M_(7) 6,671,535 41.85BARC-015057-02547 M_(7) 6,914,368 42.66 S12107-1 M_(7) 7,096,376 43.16S03624-1 M_(7) 7,774,056 45.02 BARC-044841-08824 M_(7) 7,812,440 45.13BARCSOYSSR_07_0435 M_(7) 8,194,675 46.19 Sat_244 M_(7) 8,194,675 46.19BARCSOYSSR_07_0437 M_(7) 8,243,975 46.27 Satt463 M_(7) 8,243,975 46.27BARCSOYSSR_07_0445 M_(7) 8,510,809 47.88 Sat_253 M_(7) 8,510,809 47.88S01953-1 M_(7) 8,674,220 48.13 BARC-032703-09018 M_(7) 8,935,981 48.52BARC-032703-09019 M_(7) 8,935,981 48.71 BARC-047466-12935 M_(7)9,329,297 49.17 BARC-016783-02329 M_(7) 9,628,588 50.25BARCSOYSSR_07_0518 M_(7) 9,862,864 51.86 Satt220 M_(7) 9,862,864 51.86BARCSOYSSR_07_0548 M_(7) 10,415,548 55.87 Satt323 M_(7) 10,415,548 55.87BARC-060941-16977 M_(7) 11,007,250 57.32 BARC-061507-17243 M_(7)11,259,822 56.82 BARCSOYSSR_07_0634 M_(7) 12,909,853 56.61 Satt702 M_(7)12,909,853 56.61 BARCSOYSSR_07_0683 M_(7) 14,632,112 56.16 Sat_258 M_(7)14,632,112 56.16 BARCSOYSSR_07_0690 M_(7) 14,773,940 57.44 Sat_148 M_(7)14,773,940 57.44 BARC-023101-03770 M_(7) 15,305,701 59.55BARC-023593-05477 M_(7) 15,305,813 61.29 BARCSOYSSR_07_0721 M_(7)15,307,117 61.93 Satt175 M_(7) 15,307,117 61.93 BARC-062193-17703 M_(7)15,402,867 65.75 BARC-059473-15817 M_(7) 15,607,282 66.44BARC-020517-04647 M_(7) 15,694,453 66.44 BARCSOYSSR_07_0783 M_(7)16,428,157 67.54 Satt494 M_(7) 16,428,157 67.54 BARC-015385-01815 M_(7)17,116,792 67.73 BARC-016743-03360 M_(7) 17,126,320 67.73BARC-020797-03938 M_(7) 17,175,180 67.73 BARCSOYSSR_07_0825 M_(7)17,482,347 69.18 AF186183 M_(7) 17,482,347 69.18 BARC-024721-05599 M_(7)17,600,424 69.78 BARCSOYSSR_07_0844 M_(7) 17,679,888 71.26 Satt677 M_(7)17,679,888 71.26 BARC-014217-02710 M_(7) 17,702,808 71.56BARC-012865-00400 M_(7) 18,216,965 72.63 BARC-015627-02769 M_(7)18,318,866 72.63 BARC-023229-03835 M_(7) 19,040,647 72.96BARC-024731-05607 M_(7) 19,080,789 72.98 BARC-052787-11614 M_(7)19,705,692 74.41 BARC-061433-17197 M_(7) 20,072,882 74.41BARC-057751-14916 M_(7) 20,087,945 74.41 BARC-062101-17658 M_(7)20,151,855 74.41 BARC-014249-03141 M_(7) 21,419,677 74.41BARC-061055-17021 M_(7) 24,939,884 74.41 BARC-038383-10069 M_(7)30,064,223 74.41 BARC-065185-19208 M_(7) 34,321,453 74.41BARC-058289-15194 M_(7) 35,107,980 74.78 S00111-1 M_(7) 35,590,550 79.14BARC-042549-08299 M_(7) 36,166,319 84.34 S04180-1 M_(7) 36,459,825 86.05S01008-1 M_(7) 36,638,366 87.09 BARC-055145-13086 M_(7) 36,740,933 87.68BARC-028385-05858 M_(7) 36,812,411 87.68 BARC-040209-07684 M_(7)36,978,441 87.85 BARCSOYSSR_07_1237 M_(7) 37,174,173 89.45 Satt551 M_(7)37,174,173 89.45 BARC-007320-00155 M_(7) 37,262,929 89.84BARCSOYSSR_07_1332 M_(7) 38,616,059 96.26 Sat_121 M_(7) 38,616,059 96.26BARC-026077-05254 M_(7) 38,986,948 96.96 BARC-065255-19294 M_(7)39,211,695 98.54 BARCSOYSSR_07_1431 M_(7) 40,343,666 106.12 Satt346M_(7) 40,343,666 106.12 BARCSOYSSR_07_1527 M_(7) 42,251,426 113.89Sat_147 M_(7) 42,251,426 113.89 BARC-007900-00197 M_(7) 42,385,545117.51 BARCSOYSSR_07_1556 M_(7) 42,876,624 122.55 Satt308 M_(7)42,876,624 122.55 BARC-028517-05936 M_(7) 43,709,205 127.90BARCSOYSSR_07_1644 M_(7) 44,418,256 132.42 Sat_330 M_(7) 44,418,256132.42

TABLE 45 Locus LG (ch) Physical Genetic (cM) BARCSOYSSR_03_0257 N_(3)4,554,677 23.27 Satt641 N_(3) 4,554,677 23.27 BARC-064081-18547 N_(3)4,993,899 23.85 BARC-016199-02307 N_(3) 5,808,783 25.97BARC-024681-05527 N_(3) 6,922,908 26.81 BARC-051729-11232 N_(3)8,704,943 27.18 BARCSOYSSR_03_0483 N_(3) 13,899,275 28.39 Satt485 N_(3)13,899,275 28.39 BARC-057823-14942 N_(3) 14,987,500 28.46BARC-061115-17056 N_(3) 18,958,974 29.59 BARC-050955-10882 N_(3)19,182,593 29.60 BARC-060803-16908 N_(3) 24,935,361 30.52BARC-047929-10431 N_(3) 27,977,273 30.59 BARC-047931-10433 N_(3)27,979,865 30.59 BARC-062511-17877 N_(3) 28,330,059 30.72BARC-060707-16809 N_(3) 29,090,285 30.86 BARC-052725-11576 N_(3)30,470,826 31.10 BARC-016467-02618 N_(3) 33,396,107 32.62BARCSOYSSR_03_0983 N_(3) 34,710,442 35.19 Sat_280 N_(3) 34,710,442 35.19BARC-065459-19489 N_(3) 35,169,567 37.47 BARC-013561-01160 N_(3)35,318,305 37.89 BARC-013599-01171 N_(3) 35,583,354 38.00BARCSOYSSR_03_1075 N_(3) 36,046,736 39.72 Sat_266 N_(3) 36,046,736 39.72BARC-035433-07199 N_(3) 36,785,458 42.40 BARC-039287-07269 N_(3)36,785,533 42.40 BARC-050433-09624 N_(3) 37,047,429 44.99BARC-019375-03900 N_(3) 37,309,808 45.59 BARCSOYSSR_03_1165 N_(3)37,622,075 47.24 Sat_236 N_(3) 37,622,075 47.24 BARC-021465-04122 N_(3)37,828,068 47.79 BARC-002118-00086 N_(3) 38,031,755 48.25BARC-010179-00543 N_(3) 38,032,014 49.69 BARC-018929-03038 N_(3)38,076,895 50.43 BARC-040277-07705 N_(3) 38,389,688 53.13 S12862-1 N_(3)38,491,492 53.56 BARCSOYSSR_03_1258 N_(3) 39,360,431 57.27 Satt549 N_(3)39,360,431 57.27 S12867-1 N_(3) 39,583,405 58.35 BARCSOYSSR_03_1275N_(3) 39,627,567 58.57 Satt660 N_(3) 39,627,567 58.57 BARC-038823-07342N_(3) 39,692,625 58.66 BARC-014927-01923 N_(3) 39,795,065 59.27BARCSOYSSR_03_1302 N_(3) 39,840,201 59.54 GMAB AB N_(3) 39,840,201 59.54BARC-010211-00550 N_(3) 39,840,815 59.65 BARC-048763-10711 N_(3)39,842,964 59.91 BARCSOYSSR_03_1307 N_(3) 39,934,569 60.17 Satt339 N_(3)39,934,569 60.17 BARC-024777-05683 N_(3) 40,018,491 60.48BARC-023367-05353 N_(3) 40,088,284 60.66 BARC-023365-05350 N_(3)40,115,382 60.67 BARC-046426-12582 N_(3) 40,307,332 60.96BARC-028205-05791 N_(3) 40,462,431 61.33 BARC-016485-02069 N_(3)40,585,252 61.48 BARC-029415-06172 N_(3) 40,805,854 61.80BARC-020101-04452 N_(3) 41,146,718 62.62 BARC-046692-12696 N_(3)41,231,762 63.13 BARC-046758-12733 N_(3) 41,234,262 63.13BARCSOYSSR_03_1387 N_(3) 41,732,537 65.90 Satt312 N_(3) 41,732,537 65.90BARC-013865-01261 N_(3) 41,779,870 66.30 BARC-047693-10381 N_(3)42,027,991 67.51 BARCSOYSSR_03_1412 N_(3) 42,180,031 69.28 Satt234 N_(3)42,180,031 69.28 BARCSOYSSR_03_1454 N_(3) 42,834,621 71.71 Sat_239 N_(3)42,834,621 71.71 BARCSOYSSR_03_1469 N_(3) 43,078,322 73.01 Sat_241 N_(3)43,078,322 73.01 BARC-028745-06004 N_(3) 43,242,194 73.63BARC-028539-05944 N_(3) 43,488,305 74.16 BARC-021293-04029 N_(3)43,504,295 74.29 BARCSOYSSR_03_1492 N_(3) 43,533,807 74.71 Satt257 N_(3)43,533,807 74.71 BARCSOYSSR_03_1493 N_(3) 43,594,194 76.65 Sat_306 N_(3)43,594,194 76.65 BARC-048557-10665 N_(3) 43,809,381 79.05BARC-061771-17371 N_(3) 44,172,012 80.70 BARCSOYSSR_03_1540 N_(3)44,682,640 84.45 Satt022 N_(3) 44,682,640 84.45 BARC-065687-19660 N_(3)44,732,101 85.08 BARCSOYSSR_03_1546 N_(3) 44,771,047 85.40 Sat_125 N_(3)44,771,047 85.40 BARC-027930-06703 N_(3) 44,947,921 85.82BARC-044603-08734 N_(3) 45,007,813 85.82 BARC-031999-07236 N_(3)45,098,078 86.21 BARC-060109-16388 N_(3) 45,391,016 86.91BARC-016535-02085 N_(3) 45,416,293 88.23 BARC-018125-02530 N_(3)45,517,348 88.78 BARC-014575-01582 N_(3) 45,597,671 91.19BARC-060031-16308 N_(3) 46,177,225 92.06 S04966-1 N_(3) 46,209,939 92.16BARC-029409-06170 N_(3) 46,403,735 92.72 BARC-054507-12102 N_(3)46,416,790 92.72 BARC-045143-08893 N_(3) 47,154,494 94.69BARC-030669-06920 N_(3) 47,161,222 94.69 BARC-900569-00953 N_(3)47,181,930 94.69 BARC-039729-07559 N_(3) 47,463,739 96.07

TABLE 46 Locus LG (ch) Physical Genetic (cM) BARCSOYSSR_10_1072 O_(10)38,408,903 63.99 BE801128 O_(10) 38,408,903 63.99 BARC-058227-15165O_(10) 38,679,136 65.56 BARC-054045-12290 O_(10) 38,888,903 66.82BARC-060257-16508 O_(10) 39,359,776 69.80 BARCSOYSSR_10_1148 O_(10)39,749,488 77.31 Satt477 O_(10) 39,749,488 77.31 BARC-020735-04704O_(10) 40,604,308 80.18 BARC-022409-04322 O_(10) 40,671,311 80.78BARC-042373-08248 O_(10) 40,805,085 81.69 BARC-038447-10088 O_(10)41,264,139 83.71 BARC-065285-19314 O_(10) 41,475,551 84.27BARC-056633-14536 O_(10) 41,589,284 84.48 BARC-032641-09002 O_(10)41,739,507 85.42 BARC-048879-10743 O_(10) 42,430,468 89.53BARC-008209-01052 O_(10) 42,430,516 89.80 BARC-037165-06725 O_(10)42,439,079 89.80 BARCSOYSSR_10_1339 O_(10) 42,983,878 91.36 Satt592O_(10) 42,983,878 91.36 BARC-008021-00209 O_(10) 43,283,444 92.39BARC-042813-08418 O_(10) 43,303,071 92.39 BARC-014965-01938 O_(10)43,563,691 92.39 BARC-043247-08565 O_(10) 43,812,144 92.79 S10631-1O_(10) 43,974,548 94.20 BARCSOYSSR_10_1400 O_(10) 44,136,478 95.60Satt581 O_(10) 44,136,478 95.60 S01574-1 O_(10) 44,725,777 99.50S16594-001 O_(10) 44,732,850 99.55 BARC-015925-02017 O_(10) 44,753,39699.69 BARCSOYSSR_10_1480 O_(10) 45,480,419 103.64 Sat_038 O_(10)45,480,419 103.64 BARCSOYSSR_10_1513 O_(10) 45,959,182 106.32 Satt153O_(10) 45,959,182 106.32 BARCSOYSSR_10_1517 O_(10) 46,088,357 107.31Satt243 O_(10) 46,088,357 107.31 BARCSOYSSR_10_1568 O_(10) 46,827,438110.86 Sat_307 O_(10) 46,827,438 110.86 BARC-035161-07127 O_(10)46,889,635 112.70 BARC-035395-07191 O_(10) 46,889,662 112.80BARC-018693-02992 O_(10) 47,120,942 114.57 BARC-042437-08266 O_(10)47,314,439 115.58 BARC-043129-08536 O_(10) 47,345,878 115.75BARC-008241-00035 O_(10) 47,395,171 116.29 BARC-019823-04401 O_(10)47,828,150 117.16 BARC-047374-12913 O_(10) 47,975,138 117.38BARC-046788-12746 O_(10) 48,019,353 117.38 BARC-040575-07784 0_(10)48,020,280 117.38 BARC-047426-12927 0_(10) 48,033,218 117.38BARC-065783-19748 0_(10) 48,265,046 117.86 BARC-041027-07899 0_(10)48,822,964 119.92 BARC-024123-04768 0_(10) 49,066,283 120.11BARC-048777-10716 0_(10) 49,312,430 120.78 BARC-015689-02817 0_(10)49,402,851 121.16 BARC-015167-02733 0_(10) 49,408,941 121.18BARC-015199-02739 0_(10) 49,411,491 121.18 BARC-015685-02814 0_(10)49,411,604 121.18 BARC-011313-00862 0_(10) 49,433,740 121.18BARC-015681-02809 0_(10) 49,468,084 121.41 BARC-015751-02829 0_(10)49,482,356 121.41 BARC-015683-02812 0_(10) 49,494,791 121.54BARC-030491-06877 0_(10) 49,524,668 121.73 BARC-017339-02269 0_(10)49,718,185 122.68 BARC-031993-07234 0_(10) 49,839,294 122.85 S02777-10_(10) 50,495,033 129.25 BARC-042325-08242 0_(10) 50,814,271 132.37BARC-053181-11734 0_(10) 50,825,960 132.41 BARC-056147-14126 0_(10)50,865,837 132.41 BARC-029629-06265 0_(10) 50,903,999 132.50

What is claimed is:
 1. A method of producing a soybean plant or soybeangermplasm with a late maturity phenotype, the method comprising: (a)isolating nucleic acids from a genome of a first soybean plant orsoybean germplasm; (b) detecting in the first soybean plant or soybeangermplasm at least one favorable allele of one or more marker locusselected from the group consisting of: I. at least marker locusS08590-1-Q1; II. at least one marker within a region of SEQ ID NO: 399;III. at least one marker within 5 cM of Gm07:3009018; and IV. at least apolynucleotide comprising a polymorphism at a genomic position ofGm07:3009018, wherein the at least one favorable allele is an A atGm07:3009018 for marker S08590-1-Q1; (c) selecting said first soybeanplant or soybean germplasm, or selecting a progeny of said first soybeanplant or soybean germplasm, wherein the plant germplasm or progenythereof comprise the at least one favorable allele associated with thelate maturity phenotype; and (d) crossing said selected first soybeanplant or soybean germplasm with a second soybean plant or soybeangermplasm, thus producing a soybean plant or soybean germplasm with amarker profile associated with the late maturity phenotype wherein saidproduced soybean plant or germplasm has a marker profile comprising atleast an A at Gm07:3009018.
 2. The method of claim 1, wherein saiddetecting comprises detection of a haplotype comprising markersS08590-1-Q1 and S08539-1-Q1.
 3. The method of claim 1, wherein thedetecting comprises sequencing at least one of said marker loci.
 4. Themethod of claim 1, wherein the detecting comprises amplifying the markerlocus or a portion of the marker locus and detecting the resultingamplified marker amplicon.
 5. The method of claim 4, wherein theamplifying comprises: a) admixing an amplification primer oramplification primer pair with a nucleic acid isolated from the firstsoybean plant or germplasm, wherein the primer or primer pair iscomplementary or partially complementary to at least a portion of themarker locus and is capable of initiating DNA polymerization by a DNApolymerase using the soybean nucleic acid as a template; and b)extending the primer or primer pair in a DNA polymerization reactioncomprising a DNA polymerase and a template nucleic acid to generate atleast one amplicon.
 6. The method of claim 5, wherein the admixing ofstep a) further comprises admixing at least one nucleic acid probe. 7.The method of claim 5, wherein the amplifying comprises PCR analysis. 8.The method of claim 1, wherein the detecting comprises sequencing. 9.The method of claim 1, wherein the second soybean plant or soybeangermplasm comprises an exotic soybean strain or an elite soybean strain.